Hernandez (4-2) threw only 95 pitches, but was not given a chance to record what could have been the 10th shutout and 24th complete game of his nine-year career.
Tom Wilhelmsen came on to work the ninth and wrap up Seattle's second win in a row. The Blue Jays have lost three straight.
The Mariners jumped in front with three runs in the fourth, two of them coming on the fourth home run of the season from Kyle Seager. Jason Bay added a solo shot in the sixth.
Ricky Romero took the loss in his first appearance of the year for Toronto. Romero pitched through knee and elbow problems in 2012 and was recalled from Class A to make the start against the Mariners.
Romero (0-1) gave up three runs on three hits with three walks in four innings.