The Yankees' final advantage in the game evaporated when Pettitte made what he called a "stupid" pitch to Joe Mauer with two outs in the seventh inning, challenging the Twins catcher with a four-seam fastball.
Mauer deposited the ball an estimated 382 feet over the right-field wall for his first home run of the season, tying the game at 5.
"The guy hit it out, so it makes it stupid," Pettitte said. "In that situation, I've got to stay somewhere where he's not going to hurt me, especially with a long ball. You've got two outs right there. It's as ignorant a pitch as I can throw."
The Twins gained their first lead of the night in the eighth, when Farnsworth allowed Michael Cuddyer's third hit, an inning-opening double. After a Nick Punto sacrifice bunt, Young connected with an RBI double up the gap in right-center field, giving Minnesota a one-run edge.
Farnsworth was pitching for the third time in four games, but the right-hander said he would not take his pitch selection back -- just the location, which wound up in the middle of the plate.
"I'm throwing my pitches, and I get beat on my best pitch," Farnsworth said. "It's going to happen. You've got to take the good with the bad. You just keep on going at it."
The Yankees are still looking to Farnsworth to solidify the eighth-inning mix now that Joba Chamberlain has been promoted to the starting rotation.
"It comes down to making pitches," Yankees manager Joe Girardi said. "Obviously, we didn't make the pitches we needed to make when we needed to make them. That's why we lost."
The Yankees had plenty of chances facing Twins right-hander Livan Hernandez, who was down 2-0 after the first inning on Alex Rodriguez's eighth home run of the season. Through six innings, Hernandez surrendered 13 hits, but he managed to escape with only five runs scoring.
New York left 10 men on base and stranded a runner in scoring position in every inning except the eighth, when Derek Jeter hit a ball to the right-field wall, but he was thrown out at second base on a strong throw from Cuddyer.
"We had a lot of opportunities that we didn't cash in," Girardi said. "When you leave those opportunities out there, a lot of times, it comes back to bite you."
Pettitte gave his first lead back by the third inning, after Young's first RBI double in the second inning made it 2-1. The Twins tied the game with an unearned run in the third, when Carlos Gomez singled and moved to third on a Pettitte pickoff attempt that sailed into the right-field bullpen. Alexi Casilla pushed a bunt single down the first-base line to get Gomez home.
The Yankees regained the lead in the sixth inning, pushing across two runs. With one out and a runner on first, Chad Moeller connected on a ground-rule double, and Melky Cabrera drove home the first run in the frame with a broken-bat single to left, scoring Robinson Cano from third base. Johnny Damon followed with a single through the right side to bring in New York's fourth run.
That advantage, too, was short-lived. Pettitte allowed two singles to the first three batters in the sixth inning before Craig Monroe chopped a bouncer up the middle. Cano flagged the ball and flipped it to Jeter to attempt a forceout, but Jeter couldn't hold it as Mauer trotted home to make it 4-3. Young then connected on his second RBI double out of Bobby Abreu's reach in right field, tying the game at 4.
"We didn't necessarily lose that game because of Kyle Farnsworth," Girardi said. "We had many opportunities tonight. We didn't execute."
Rodriguez would also briefly give New York a lead -- its last -- in the seventh by doubling on Hernandez's final pitch and scoring on a Jason Giambi fielder's choice. The throw from first baseman Justin Morneau beat Rodriguez to the plate, but Mauer was slow with the tag, as Rodriguez was ruled safe by home-plate umpire Gary Darling.
The Yankees completed their seven-game road trip to Baltimore and Minnesota with a 3-4 showing, falling one game below .500 at 28-29. They return home on Tuesday, when Chamberlain will make his first Major League start to open a three-game series against the Blue Jays.
"We should have had a much better record on this road trip, and I'm not happy with it," Girardi said. "We have to start playing better, and that's the bottom line."