Bautista hit a 1-2 pitch from reliever Brandon Kintzler into the Brewers' bullpen in right field. The homer made a winner of R.A. Dickey (10-12), who gave up five runs in 5 2-3 choppy innings.
Dickey left after Carlos Gomez's two-run homer in the bottom of the sixth made it 7-5.
Colby Rasmus also homered for Toronto, which outhit the NL Central leaders 15-10.
Jimmy Nelson (2-4) took the loss after allowing the first two runners to reach in the sixth.
The Blue Jays, who were a season-high nine games out of first in the AL East entering the day, finished 2-6 on their road trip.
The Blue Jays' bats broke out for seven runs and eight hits between the fifth and sixth innings. Josh Thole and Munenori Kawasaki got the rally in the sixth with back-to-back doubles before Bautista hit his 24th home run.
Milwaukee had the potential go-ahead run up with one out in the eighth and NL doubles leader Jonathan Lucroy at the plate. The .304 hitter hit a hard bouncer to reliever Dustin McGowan for an easy 1-6-3 double play.
Facing a former Cy Young Award winner for the fourth straight start, Nelson gave up four runs and nine hits in 5 2-3 innings.
Dickey, who won the Cy Young in 2012 while with the Mets, wasn't much better after allowing eight hits. Gerardo Parra had a double and triple off Dickey, making him a career 6 of 9 off the knuckleballer.
Blue Jays: RHP Brandon Morrow, on the disabled list since May 3 because of a torn tendon in his right index finger, has "cut it loose" in throwing side sessions but isn't at full strength, manager John Gibbons said. Toronto hopes Morrow will be ready in September, likely out of the bullpen.
Brewers: Manager Ron Roenicke said he hasn't started discussions about what to do with Mike Fiers once RHP Matt Garza returns from the disabled list with a rib cage muscle injury. Garza will go back into the rotation when ready, likely in early next month. Fiers is 3-0 with an 0.86 ERA in three starts since being called up Aug. 9 from Triple-A.
Blue Jays: After an off-day, Toronto returns home to face the Tampa Bay Rays on Friday. RHP Marcus Stroman (7-4) will try to rebound from a rough outing, after he failed to get out of the first and allowed five runs on Aug. 15 to the White Sox
Brewers: Milwaukee gets its second off-day in four days Thursday. RHP Yovani Gallardo (8-6) has a chance to put the struggling Pirates in deeper trouble in the NL Central when Pittsburgh begins a three-game series Friday.