Toronto's sixth win in seven games moved the Blue Jays ahead of the Twins and into the second AL wild-card spot.
Minnesota has been held to just one run in four of its past five games, losing all four. The Twins are 5-12 since the All-Star break.
Hughes (10-7) lost for the first time since June 8 against Kansas City, snapping a streak of six straight winning decisions. He allowed five hits and three runs in 5 2-3 innings.
Hughes walked two batters, just the second time this season he has walked more than one, and uncorked his first wild pitch of the season. Hughes walked two batters on May 4, against Oakland.
Donaldson hit his 28th home run in the first, connecting on a 2-2 pitch. It's the eighth time this season he's homered on a two-strike count.
Donaldson has a 22-game hitting streak against the Twins. It's baseball's longest active streak for any player against an opponent.
Tulowitzki made it 2-0 with a leadoff shot in the third, his second since joining Toronto last week.
The Blue Jays were without manager John Gibbons, who served a one-game suspension for coming back on the field when the benches and bullpens cleared in the eighth inning of Sunday's win over Kansas City. Gibbons had been ejected for arguing with home plate umpire Jim Wolf one inning earlier.
Bench coach DeMarlo Hale took over for Gibbons against the Twins.
Sanchez was suspended three games for sparking the melee by throwing at Kansas City's Alcides Escobar. Sanchez is appealing his penalty.
Twins: RHP Tyler Duffey will make his major league debut in place of injured LHP Tommy Milone (elbow). Duffey went 6-8 with a 2.66 ERA in the minors, starting eight games at Double-A and 13 at Triple-A.
Blue Jays: Durability and consistency remain elusive for RHP Drew Hutchison (9-2, 5.42 ERA), who has won only once in five starts and hasn't reached the seventh inning since June 6 against Houston.