Mike Carp added a two-run single in the opening inning for Seattle, which rebounded from Friday's 6-4 loss in the opener of this three-game series.
Despite the early 5-0 lead on Saturday, the Mariners ended up taking a narrow victory.
After Hernandez pitched a scoreless seventh, Boston slugger David Ortiz nearly hit a game-tying homer off Jamey Wright in the eighth. But Wright managed to keep the Red Sox off the scoreboard, and Brandon League worked the ninth for his 28th save.
Josh Beckett (9-5) took the loss after allowing all of the Mariners' runs, and lasted five innings.