Updated (5:36 p.m. with quotes from the post-game interviews): Derek Jeter really set the tone for this one in the first inning. A walk and a balk landed him on second base with Nick Swisher up, and then Derek got greedy. He took off for third, and while the replays showed he may have gotten his hand in before the tag, the throw beat him. “Out!” said the umpire.

An argument ensued, and as Jeter later explained during the post-game interviews, the ump had some interesting explanations for the call. Jeter alleges that Marty Foster said he made the out call because the throw beat him by so much. “I was told I was out because the ball beat me, and he didn’t have to tag me,” Jeter said to the reporters. “I was unaware they had changed the rules.”

If that’s really how it went down, Foster has some explaining to do. That’s a pretty outrageous statement for an umpire to make. Until instant replay review is instituted in baseball on a wider level, that subjective decision is part of the game, and it killed the Yanks in the first.

On the next pitch, Nick Swisher laced a single into center field. If we discount the fact that nothing in baseball is a predestined event, Jeter could have scored. In addition to the bad call, what also irked me about Jeter’s decision — and I’m pinning this one on Jeter’s choosing to try for third — was how little it could have helped the Yanks had he been safe.

Based on the 2009 Run Expectancy Matrix, teams this year with a runner on second and no one out are expected to score 1.10 runs. Teams with a runner on third and no one out are expected to score 1.32 runs. Meanwhile, a team with one out and no one on is expected to score 0.29 runs. The marginal reward for the steal of third is just 0.22 runs while Jeter’s making the first out at third base cost the Yanks 0.81 runs. Even though he was technically safe, it just doesn’t make sense for Jeter to try that risky move with no one out and the Yanks’ heart of the order due up, and we don’t need the run expectancy spreadsheet to tell us that. In that situation early in the game, it’s just not worth the risk.

The rest of the game was similarly frustrating. Andy Pettitte needed just six pitches — five of them strikes — to get through the first and then used 103 more to get through the next 5+ innings. Of those, 53 were strikes and 50 balls. He just didn’t have his best stuff, and Tony Pena, managing for the ejected Joe Girardi, probably shouldn’t have left him in to start the 7th with his pitch count pushing 100.

But Andy Pettitte is Andy Pettitte. It’s frustrating to watch him alternate good starts and bad starts, but at the same time, he’s the team’s fifth starter. Even without his best stuff, he gave the Yankees a chance to win it. They just couldn’t capitalize. We could blame the umpires for a bad call in the third that eventually led to a two-out, three-run home run off the bat of Alex Rios, but blaming the umps gets us nowhere. That’s just part of the game. Pettitte, and not the umpires, threw an 0-1 fastball into Alex Rios’ wheelhouse.

The loss may belong to Pettitte, but I’d be remiss to leave out a mention of Brian Bruney. The former 8th Inning Guy came in with a runner on first and no outs in the 7th. The Yankees needed Bruney to slam the door, and he threw it wide open. After a strike out, back-to-back doubles brought home an inherited run and one of his own. The Blue Jays had a 7-1 lead, and while Bruney would get another out and issue a free pass before getting the hook, the game was nearly out of reach. Where Bruney fits into the pen right now is anyone’s guess, but it won’t be in high leverage situations until he earns it.

In the end, the Yanks tried to mount a comeback. They plated two in the 7th, one in the 8th and two in the 9th, but it would not be enough. Nick Swisher didn’t come through with two outs and the bases loaded. Eric Hinske struck out swinging on a 3-2 slider from Justin Frasor with the tying run on first. Sometimes, the Comeback Kids can’t comeback.

We can’t complain too much about the homestand. The Yanks have won four straight series, and if they go 3-1 every four games, we’d be happy. But at the same time, you want to see them squash some teams along the way. For the second straight series, they had a sweep within their grasp but could not close the door. Today, they had their chances but went just 2 for 11 with runners in scoring position and left 11 runners on. From Jeter to the umpires to Pettitte and Bruney to the failed ninth inning comeback, it was one frustrating game.

Through two innings on Sunday afternoon, the Yankees found themselves enjoying the good life. They had put on 10 runners and had scored four runs while Joba Chamberlain had done a decent job recording the first six outs.

In the third and fourth innings, though, the wheels fell off. In the third, a few hits and a home run brought the Blue Jays to within a run. All three Toronto runs scored with two outs. Worse still was Joba’s climbing pitch count. It took him 65 pitches to record the first nine outs of the game, and again, the Yanks’ youngster couldn’t put hitters away .

Joba would get just two more outs and use 31 more pitches before finding himself out of the game with two outs in the fourth. A single by Lyle Overbay followed by a Vernon Wells fly out set the stage for a play that would echo throughout the game. Cody Ransom misplayed a potential double-play ball, and Joba couldn’t get out of the inning. With two on, Joba got the second out, but then the Blue Jays let loose. Double, single, home run, single. 8-4 Toronto. Joba out; Albaladejo in.

Chamberlain’s final line shows just three earned runs, but the rest of it is downright ugly. He allowed nine hits and a walk in 3.2 innings. He struck out just one and allowed eight runs to score, all with two outs. He threw 86 pitches and wasn’t particularly wild. In fact, a 53/33 ball-to-strike ratio is a bit of an improvement over Joba’s recent efforts.

And yet, this time he couldn’t escape with his 92-mile-per-hour fastball. He couldn’t finish off hitters; he couldn’t finish off innings; and the Blue Jays instead finished him off in short order. As I mentioned last week, Joba’s velocity just isn’t where it needs to be. He threw just a handful of pitches at about 94mph and sat at 92.4, according to Gameday. His peak is down by about 4-5 miles per hour over last year, and his average is down by around 3-4 miles per hour as well.

In the end, today wasn’t a step back for Chamberlain as much as it was a course correction. For weeks, he’s been throwing too many pitches, putting too many runners on and getting away with it. Today, it came back to bite him, and he lost it bad. It’s definitely becoming a problem. Now, the solution to the Joba Problem isn’t to move him to the bullpen. He had these velocity problems in the pen last year, and as Mike will explain on Monday morning, the bullpen should be out of the question. The solution is to find those missing miles-per-hour. Where they are, I do not know.

Meanwhile, with Joba out, the Yankees never said die. Led by a four-hit attack by Derek Jeter and a big three-run shot by Hideki Matsui in the bottom of the disastrous fourth, the Yanks pulled a Roger Federer. After a grueling 3 hour 44 minute affair, the Yanks won by two.

With the offense as loaded as it is, no game is really over for this team, and for that, we can thank the bullpen. Sunday’s game belonged to Al Aceves. He utterly dominated the Blue Jays for four innings and threw just 10 of his 43 pitches out of the strike zone. He allowed one hit and struck out five. I shudder to think where the Yanks would be without him.

Aceves put the exclamation point on a stellar weekend of relief pitching. In three games against the Jays, the Yanks’ pen has twirled 14 innings. They’ve given up one earned run on eight hits and four walks while striking out 12. Considering how badly the pen fared in April, this overhauled bullpen led by Mo, the Phils and Aceves has been all sorts of great.

When the dust settled, the Yanks won. They held steady with Boston who pulled off a late-game comeback of its own, and gained a game on the Rays. They play again at 1:05, and with this win behind us and another game in a few hours, going back to work on Monday isn’t as bad as it could be.