Toronto came back in the next half-inning when Munenori Kawasaki got a one-out single off Orioles' starter Miguel Gonzalez and Darren O'Day came in to pitch.
After Rajai Davis grounded out, Bautista smacked a pitch down the left field line that curled around the foul pole for a decisive two-run clout.
Casey Janssen tossed a 1-2-3 ninth for his 17th save as the Blue Jays won a 10th consecutive game for the first time since 2008.
Toronto starter Chien-Ming Wang allowed just one run on five hits over 6 1/3 innings.
Gonzalez (5-3) surrendered three runs on three hits over 7 1/3 frames, walking three and striking out five for Baltimore.