Hernandez exited after six innings with a 3-1 lead, having outpitching CC Sabathia in the first matchup between the former Cy Young Award winners.
Hernandez, however, appeared to hurt himself in the sixth when he fielded a comebacker, pivoted and threw to second for a forceout. The Seattle ace twice kicked his left leg near the mound, trying to get loose, and seemed to say "ouch" a few times.
Manager Eric Wedge and a trainer visited Hernandez and left him in. Overbay followed with an RBI double that made it 3-1. There was no announcement on whether Hernandez had tweaked something, was injured, or was pulled after 97 pitches.
Hernandez allowed one earned run in another strong outing at Yankee Stadium, and leads the AL with a 1.53 ERA. Sabathia, who had won his last eight starts against Seattle, struck out 10 in 6 1-3 innings while giving up 10 hits.
Raul Ibanez hit a two-run homer for Seattle in his return to Yankee Stadium. New York star Curtis Granderson came off the disabled list and went 0 for 3 with a walk in his season debut.
Down 3-1, the Yankees rallied for three runs in the seventh to win for the seventh time in eight games.
Mariners reliever Yoervis Medina gave up a leadoff single to Chris Nelson, who went to second on a wild pitch. Charlie Furbush (0-2) entered with one out and walked Brett Gardner before Cano tied it with his double off the base of the wall in right-center.
Vernon Wells was intentionally walked, Granderson walked to load the bases and Overbay hit a sac fly to center that put the Yankees ahead.
Shawn Kelley (2-0) got two outs in the seventh. Mariano Rivera pitched the ninth to remain perfect in 16 save chances this season.
Granderson broke his right forearm in his first at-bat of spring training, and the public-address announcer said "Welcome back" when introducing the starting lineups.
Granderson was the first of the injured Yankees' stars to return to the team. Derek Jeter, Mark Teixeira and Alex Rodriguez still haven't played this year.
Ibanez got a nice ovation before the game from fans who remembered his clutch homers last October for the Yankees when he connected this time, the crowd responded with a mix of boos and calls of "Ra-uuuul."
Hernandez was involved in a weird play in the fourth when he ran over to cover first base on Overbay's grounder to the right side. Hernandez was called for obstruction and charged with an error when Overbay ran into him near the bag as first baseman Kendrys Morales took the throw for an apparent out.
Seattle took a 1-0 lead in the third on Kyle Seager's double.
NOTES: The Mariners committed two errors in a game for the first time this season. C Kelly Shoppach made a wild throw to first, trying to get Nelson when he struck out and reached on a wild pitch in the third. ... DH Travis Hafner was out of the Yankees' lineup because of a sore right shoulder. New York manager Joe Girardi said Hafner would have an MRI and get a couple days off as a precaution.