Hernandez (4-1) won for the first time in more than a month. He took a shutout bid into the seventh inning, then gave up a three-run double to Ryan Hanigan with two outs and was pulled.
As Hernandez was leaving, he complained to plate umpire Mark Ripperger and was tossed for the first time in his career.
James Jones doubled, singled and scored in each of the first three innings as the Mariners took a 9-0 lead. Robinson Cano drove in two runs.
Stefan Romero homered, doubled and singled for Seattle. Justin Smoak hit a two-run homer and Mike Zunino added a solo shot.
The rare back-to-back replays came in the first inning as Cano and then Corey Hart both barely missed home runs on flys that hit the yellow line atop the fence and bounced back. Umpires ruled both balls in play, and their calls were confirmed.
Cano wound up with a double on his drive to left field, Hart was thrown out trying for a double on his shot to right.
Cesar Ramos (1-2) was tagged for 11 hits and nine runs in the first three innings, and pitched into the seventh.
Tampa Bay didn't help itself, tying a team record by making three errors in the second inning. The Rays also had an error in the first inning.
Hernandez rebounded from a rough last four starts. It was his first start for the Rays since Aug. 15, 2012, when he tossed a perfect game at Safeco Field.
That day was the crowning achievement of Hernandez's career; Monday was just a chance for Hernandez to rediscover his groove.
The Seattle ace was slowed recently by a flu bug. Finally healthy, Hernandez began finding the same success that had him going so well to begin the season.
After not striking out anyone in his last start against Oakland, Hernandez fanned seven. He didn't walk a batter and gave up eight hits.
Hernandez retired the first five batters to run his hitless streak against the Rays to 34 batters before Wil Myers reached on an infield single with two outs in the second.
Despite getting knocked around, Ramos was forced to stay on the mound and save Tampa Bay's bullpen. Ramos was able to get through 6 2-3 innings and didn't allow a hit after the third.