Jason Kubel homered and Brendan Harris had three hits for the Twins.
Cubs starter Randy Wells (0-3) allowed four runs in 3 2-3 innings, his shortest outing of the season.
Despite missing all of April with a back injury, Mauer matched his single-season high with his 13th home run. Still, Friday's two-run, third-inning homer was only his second in 16 games following a torrid three-week stretch after he came off the disabled list.
The two-time AL batting champion boosted his average to .413 and, in a rarity for a visiting player at Wrigley Field, heard chants of both "M-V-P!" and "Let's go, Mauer!"
The Cubs' Milton Bradley wasn't so beloved by the home fans even though his two-run double in the sixth off Slowey halved what had been a 4-0 deficit.
In the seventh, he lost Jason Kubel's pop-up in the sun for a single and got a late jump while failing to catch Michael Cuddyer's RBI bloop double for a 5-3 Twins lead
- and then it got worse.
With Nick Punto on third, Harris on first and one out in the eighth inning, Bradley caught Mauer's flyball and, thinking the inning was over, posed for several seconds before throwing the baseball into the seats. As Punto scored easily on the sacrifice fly to make it 6-3, Harris was awarded third base on Bradley's error as boos cascaded down from every section of the ballpark.
Bradley, a $30 million free agent who has struggled at the plate, battled injuries and argued with umpires, has been booed often this season.