Ian Happ scored on Baez's single up the middle after drawing a walk and advancing on a groundout. On Friday, Baez drove in three runs in the Cubs' 7-4 series-opening victory over the Blue Jays.
Happ also homered and had an RBI single for the Cubs (65-57), who hold a slim lead in the National League Central and won the first two games of the series against the Blue Jays (59-64).
Cubs starter Jose Quintana (4-2) struck out eight and allowed two runs, four hits and two walks (one intentional) in six innings. He was 6-2 with a 1.77 ERA in nine previous career starts against Toronto.
Wade Davis posted his 26th save in 26 chances. He has converted his last 31 chances since September with Kansas City.
Nick Tepesch allowed two runs and five hits in 3 2/3 innings in his third appearance with Toronto since he was traded from Minnesota on July 23 for cash considerations.
Happ hit his 18th home run to lead off the bottom of the fourth inning and tie the score at 2.
The Cubs had runners at second and third after a Quintana sacrifice, but Jon Jay struck out looking against reliever Danny Barnes (2-4) to end the inning.
Jay disagreed with the call from home plate umpire Joe West.
Toronto went ahead 2-1 on Raffy Lopez's two-run single in the top of the fourth. Pillar singled and Darwin Barney doubled before Lopez singled to drive them in.
The Cubs loaded the bases via two walks and a hit batter in the first inning but scored just one run on a Happ single. Toronto got out of the inning with a double play.
The Blue Jays are 8-6 all time against the Cubs, with their last visit to Wrigley in 2005.
NOTES: The Cubs claimed C Rene Rivera off waivers from the New York Mets. He has a .215 batting average with 34 home runs in parts of nine major league seasons with Seattle, Minnesota, San Diego, Tampa Bay and New York. He was batting .230 with eight home runs and 23 RBIs with the Mets this season. Cubs manager Joe Maddon praised Rivera's defense and throwing. ... RHP Aaron Brooks was designated for assignment to make room on the Cubs' 40-man roster. He was 8-9 with a 6.20 ERA at Triple-A Iowa. ... The Blue Jays called up RHP T.J. House because of a taxed bullpen. He was 9-11 with a 4.27 ERA at Triple-A Buffalo. ... Toronto optioned LHP Tim Mayza to Triple-A. He was 0-0 with a 6.00 ERA in three appearances. ... Blue Jays 3B Josh Donaldson moved to shortstop in the eighth inning to play the position for the third time in his career. ... C Mike Ohlman cleared waivers and was outrighted to Triple-A Buffalo, the Blue Jays announced. He was designated for assignment Wednesday.