His solo homer in the bottom of the sixth inning gave Toronto a 3-1 lead, and after Mark Texeira's two-run blast in the top of the eighth drew Atlanta within 6-5, Wells' two-run double capped the scoring.
Joe Inglett had two hits and two RBI, while four Toronto players knocked in one run each, including Rod Barajas, who hit a solo homer in the fifth.
Four players had two hits for the Blue Jays, who had lost nine of 12.
Winner John Parrish (1-0) allowed an earned run and four hits in six innings.
Four other Atlanta players had one RBI. Gregor Blanco had four hits and Kelly Johnson two for the Braves, who have split their last four games.
Losing pitcher Tim Hudson (8-6) surrendered six earned runs on seven hits in five innings.