Napoli's blast in the first inning put Boston ahead 3-1 and American League East-leading Red Sox went on to collect 11 hits, dealing the Yankees' hopes for an AL wild-card berth a hard blow with a three-game series sweep.
Buchholz (11-0) remained unbeaten on the season in his second start after missing more than three months with a strained neck. He limited New York to one unearned run on two hits, walking four and striking out three.
Ivan Nova (8-5) was battered for five runs (four earned) on six hits over four innings for the Yankees, who fell three games off the wild-card pace with Cleveland and Baltimore ahead of them.
Notable deaths of 2014 [PHOTOS]
Michael Sam cut from the Dallas Cowboys