His go-ahead single came with one out in the bottom of the eighth after Adam Lind's only hit, an RBI double, created a 1-1 tie.
Toronto benefited from two stolen bases and a wild pitch by losing pitcher Scott Linebrink (1-2) in its manufactured rally.
Marco Scutaro had three of 11 hits, while Bautista and two others had two hits for the Blue Jays, who beat Chicago at its home field, Rogers Centre, for the eighth straight time.
The winner was rookie starter Robert Ray (1-1), who earned his first major league victory by giving an unearned run and just three hits in eight innings.
Closer Scott Downs recorded his fourth save.
Chicago's run scored on a first-inning throwing error by Raul Chavez.
Three players had one hit for the White Sox, who have lost three in a row.
Copyright 2009 by United Press International.