He was gunning for a career-high 10th win and fourth straight.
"The pitch to Nunez was just about neck high and off the plate about a foot," Vargas said. "He just threw his bat at it and [the ball] squirted through the hole.
"When something like that happens, you can't do a whole lot about it."
Vargas retired 15 consecutive batters between the first and sixth innings, giving the Mariners' offense a chance of overcoming a rocky start for both starters.
The first inning consumed almost 30 minutes and featured the longest home run to right field in the Stadium's one-plus year history.
The sellout crowd was still digesting the leadoff home run Ichiro Suzuki hit in the first inning, his second first-inning home run of the season and 32nd of his career, when Russell Branyan sent a 3-and-1 pitch from Yankees right-hander Javier Vazquez up, up and far away -- into the upper deck.
It was first time anyone has reached that level of seats.
Just like Friday night, when Felix Hernandez had a lead when he threw his first pitch, Vargas was up by two runs when he went to work. Unlike the previous night, the lead vanished quickly.
The Yankees retaliated in the bottom of the first with four runs. Vargas surrendered an infield single to Derek Jeter, a double to Mark Teixeira, a two-run single to Robinson Cano and a two-run home run to Jorge Posada.
"The ball Teixeira hit for a double down the left-field line I left over the plate too much, and the changeup up to Posada I just hung," Vargas said. "If I could pinpoint a couple of things, those would be them.
"Otherwise, I stayed with the game plan and things went better."
You might say that.
He retired 15 consecutive Yankees between an inning-ending strikeout of Kearns in the first and Cano's two-out single to right in the sixth. But Vargas struck out Marcus Thames to end the inning and fanned Posada to start the seventh inning -- an inning he didn't finish.
Three consecutive singles scored the go-ahead run, reliever Jamey Wright was welcomed to the fray with a run-scoring single by Jeter, then came a walk and sacrifice fly, capping the three-run rally.
"[Vargas] did a nice job keeping us right there in the game [and] at some point, you just want to give him the opportunity to win or lose the game," interim manager Daren Brown said.
"I thought it was a bit of a rough start, but after the first inning he was really good," the skipper added. "Between the first and seventh innings, he was throwing as well as I've seen him throw."
The Mariners, showing considerable spunk of late, struck back in the third inning when Ichiro led off with his second home run -- his first multihomer game this season and fifth of his career. Two outs later, consecutive singles by Jose Lopez, Franklin Gutierrez and Casey Kotchman produced the tying run.
A few feet kept the Mariners from having a much more productive inning.
Michael Saunders just missed hitting his first career grand slam, sending right fielder Yankees Nick Swisher to the warning track to catch his towering drive.
"Offensively, we swung the bats well," Brown said of Seattle's 12-hit attack. "We hit three home runs, but you would have liked them to have been with runners on base."
The Mariners did not go down quietly. They put two runners on in the eighth inning, forcing Yankees manager Joe Girardi to summon closer Mariano Rivera, who retired Saunders on a popup.
One-out singles by Ichiro and Chone Figgins led to a run in the ninth off Rivera.
The eighth inning, though, was noteworthy from a defensive standpoint.
Mariners first baseman Casey Kotchman went into the game on a Major League-record 274 consecutive error-free games -- the longest such streak for a first baseman in history.
But he could not come up with a hot shot hit by Curtis Granderson with one out in the eighth and was charged with an error. It was his first miscue in 2,379 fielding chances.