Hernandez (7-1) toed the slab for Seattle and was charged with one run on four hits and two walks with nine strikeouts over 8 2/3 innings in the win.
C.J. Wilson (6-4) opposed Hernandez and allowed three runs on five hits with two walks and five strikeouts over 7 2/3 frames.
Justin Smoak singled to lead off the second, then Kyle Seager walked before both runners advanced on a John Buck groundout. Wilson got Dustin Ackley to pop out to second, but couldn't get out of the jam, allowing a two-run single to Zunino as the M's jumped on the board.
Zunino delivered some insurance in the eighth with a solo shot to left center which made it 3-0.
Hernandez faced the minimum in six of his first eight innings before running out of gas in the ninth.
Hernandez struck out Collin Cowgill for the first out, then Howie Kendrick flied out to center.
Mike Trout extended his hitting streak to nine games with his two-out single to left and later scored on Albert Pujols' double to right that ended Hernandez's night.