Thome hit his 29th homer this season with a man on and two outs off starting and losing pitcher Tim Wakefield (8-9). The homer was the 536th in Thome's career, tying him with Mickey Mantle for 14th on the all-time list.
Winning pitcher Gavin Floyd (15-6) gave up one earned run and seven hits in 6 2/3 innings with two walks and five strikeouts.
Closer Bob Jenks followed two other relievers to record his 27th save.
Boston's Jacoby Ellsbury had three hits and one RBI. Jed Lowrie had one RBI and five others had one hit for the Red Sox, who have lost twice in the last six games.