The Yankees won twice in the three-game series, but still trail the first-place Red sox by 9 1/2 games in the American League East.
New York starter Andy Pettitte (3-3) lowered his ERA to 2.66 by allowing one run on eight hits in seven innings. He has a career record of 14-6 against Boston.
Schilling (4-2) gave up 12 hits and six runs through six innings.
The Yankees got a home run from Doug Mientkiewicz, three hits along with one RBI from Johnny Damon, and a triple, two RBI and two runs scored from Derek Jeter. Jeter passed Joe DiMaggio for fifth place on the Yankees' all-time hits list.
New York scored three times in the first inning before Schilling recorded an out -- two of the runs coming on Matsui's line-drive homer down the line in right.