Gonzalez (8-2) issued two runs on three hits and two walks. He struck out five as National League Central-leading Washington clinched their three-game series at Fenway Park.
Three Nationals relievers combined for 1 2/3 scoreless innings and Tyler Clippard picked up his seventh save for Washington, which won for the fourth time in five games.
Daisuke Matsuzaka (0-1) absorbed the loss in his first start in nearly a year following elbow surgery. The right-hander struck out eight while yielding four runs on five hits in a five-inning stint.
Jerrod Saltalamacchia drove in two runs for the Bosox.