Seager tattooed a 3-0 fastball from Padres starter Tyson Ross for a three-run homer in the first inning.
The Mariners added two more runs in the second — one coming on a Brad Miller homer — and one-time San Diego ace Chris Young and the bullpen took it from there.
Gywnn, the greatest player in Padres' history, died earlier in day, at age 54, from complications resulting from salivary gland cancer. The Mariners paid tribute to the Hall of Famer in a video tribute and a moment of silence.
The Mariners also marked the infield with Gwynn's No. 19 in the “5.5 hole” — the space between shortstop and third base where so many of Gwynn's 3,141 career hits found daylight.
Then it was down to business.
Young (6-4) bounced back from his first career Safeco Field loss by pitching six shutout innings before handing a five-run lead to Joe Beimel to start the seventh.
Beimel worked around a leadoff walk in seventh but exited after a leadoff walk in the eighth. Tom Wilhelmsen retired the next three hitters before surrendering the shutout on Carlos Quentin's leadoff homer in the ninth.
Ross (6-6) steadied after a shaky start — three runs in the first and two more in the second — and pitched into the sixth. Even so, that early damage was significant: five runs on seven hits and six walks.
The Mariners (36-34) have now won two in a row after a five-game skid dropped them back to .500. They complete the northern half of their “natural rivalry” series against the Padres at 12:40 p.m. today.
The two teams play Wednesday night and Thursday afternoon in San Diego.
Young's shakiest inning was the first when he permitted two one-out singles, but he escaped with no damage in part because third baseman Kyle Seager ran down Yonder Alonso's two-out foul pop near the stands.
The Mariners then jumped Ross for three quick runs.
Endy Chavez led off with a single but was erased at second on a James Jones bunt. Jones stole second and third while Robinson Cano drew a walk. Ross then fell behind 3-0 on Seager and offered up a get-me-over fastball.
Seager was swinging and lined the ball into the right-field seats for a three-run homer. It was the first homer by a Mariner on a 3-0 count since John Jaso on Aug. 10, 2012 against Ervin Santana at Angel Stadium in Anaheim.
The Mariners extended their lead to 5-0 in the second inning. First, Miller rocked a no-doubt, one-out homer to right. Jones then reached on a fielder's choice, stole second and scored on Cano's two-out double to left.
The lead could have been bigger.
The Mariners did nothing with a leadoff walk in the third, left runners at first and third in the fourth and left the bases loaded in the fifth.
So it was still 5-0 when Will Venable opened the San Diego sixth with a single past first baseman Logan Morrison. An errant pickoff throw byYoung moved Venable to second.
Young retired the next three hitters.
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