Buchholz (8-0) yielded just two hits and a walk while striking out four for Boston, which was leading in the middle of the sixth inning when the game was called after three lengthy rain delays.
The right-hander, pitching after 10 days of rest due to a shoulder problem, threw 43 of his 71 pitches for strikes and lowered his ERA to an American League-best 1.62 as the AL East-leading Red Sox took two-of-three from the Yankees.
Jose Iglesias and David Ortiz each socked a solo homer for Boston.
Yankees starter Hiroki Kuroda (6-4) was tagged with the loss after surrendering three runs on eight hits over 5 1/3 innings.
New York fell for the seventh time in eight games and dropped into fourth place in the division, four games behind Boston.