The Yankees took a 3-1 lead into the seventh with Hughes having allowed only four hits. But the right-hander started the inning by allowing a leadoff single to Ryan Doumit, then issued a walk to Chris Parmelee, who had brought home Minnesota's first run with a fourth-inning double. Hughes induced a popout from Trevor Plouffe before surrendering an infield single to Jamey Carroll that loaded the bases.
Hughes then buckled down to fan Pedro Florimon for the inning's second out. By then, Hughes had thrown 26 pitches in the inning and 99 in the game, and manager Joe Girardi had seen enough.
"He started missing up [in the zone]," Girardi said of Hughes. "A lot of times, you start to worry when that starts to happen."
Girardi pulled Hughes in favor of the left-handed Logan against left-handed-hitting outfielder Denard Span. But both Hughes and catcher Russell Martin said they felt the right-hander had enough left in the tank.
"Any time, you want to finish an inning," Hughes said. "Especially when you get the little momentum of striking a guy out. You want to get the next guy. But you don't worry about those decisions. Just live with them."
Girardi cited Logan's previous success against Span -- who had gone 0-for-4 with a walk in his career against the lefty -- as another reason for the change.
Span had been 0-for-3 with three groundouts against Hughes on the night.
"It had been a struggle so far in that inning [for Hughes]," Girardi said. "He had a walk, a 3-2 count, a long at-bat. Booney had had a ton of success against Span. It didn't work."
Logan's outing went awry from the first pitch, which skipped to the backstop and allowed Doumit to score Minnesota's second run.
Logan and Span battled to a full count before Span lifted a double to the right-center-field gap, scoring Parmelee and Carroll to give Minnesota a 4-3 lead. Two batters later, Joe Mauer singled to tack on another run. Logan induced a popout from Justin Morneau to finally end the inning.
"I like going in there in those situations," Logan said. "I'm upset, A, that we lost and B that I gave up those runs. I had four lefties to get out in a row, and I only got one of them out.
"There's no excuse. I just didn't have my stuff tonight."
Andruw Jones' pinch-hit homer -- the fifth of his career -- with two outs in the top of the ninth cut the Yankees' deficit to one run. But Twins closer Glen Perkins retired Jayson Nix with a strikeout to seal the victory.
Swisher opened up a 2-0 lead for the Yankees in the fourth with his 24th homer of the year and fourth in six games. Martin added his 19th of the season in the seventh, matching his career high for homers, set in 2007 as a member of the Dodgers. All 10 of New York's runs in the first two games of the series came via the home run.
Derek Jeter opened the game with a single to extend his hitting streak to 19 games, his longest since he hit in 19 straight games from May 5-25, 2007. Jeter is hitting .365 during the streak, which dates to Sept. 4.
Robinson Cano -- who entered the game hitting .224 in September -- went 3-for-3 with a walk for his fifth career three-hit game against the Twins.
"It was a good day [for me], but it's not good enough because we lost the game," Cano said. "It's always good when you win the game."
Three of the four runs scored by the Twins in the seventh were charged to Hughes, who allowed four runs on six hits and a walk over 6 2/3 innings. The right-hander, who had won his last three starts, fell to 16-13 on the season.
Span tweeted to Orioles outfielder Adam Jones earlier in the day, "We trying to help y'all out man."
Span and the Twins were successful, at least on Tuesday.
"I saw they lost tonight, and we were able to get a win to kind of help them out a little bit," Span said of the Orioles. "So we'll see ... if we can beat CC [Sabathia] tomorrow, maybe I'll text [Jones] and see if he'll buy me dinner next Spring Training."