Thomas went 4 for 4 with two RBI doubles. He drove in Oswaldo Arcia both times, including in the eighth when his drive off the tall wall in right field against Antonio Bastardo (2-2) tied the game.
Delmon Young and Ben Revere hit RBI singles for the Phillies against their former team, but starter Mike Pelfrey kept the game close with a season-high seven innings and Glen Perkins pitched a perfect ninth for his 15th save in 17 tries.
Arcia went 3 for 3 and scored three times, all after hits that led off an inning. Eduardo Escobar's bunt that followed the tying hit by Thomas had just the right amount of backspin to nestle into the grass along the first-base line for a single, putting the Twins in position to take the lead.
Justin De Fratus relieved Bastardo and retired Pedro Florimon on a hard line drive right at second baseman Freddy Galvis, but the right-hander let one get away that reached the backstop and Thomas scored easily.
The Phillies began the game with a 4.48 ERA for the bullpen, the third-worst mark in baseball.
Phillies starter Tyler Cloyd, the prized prospect called up last month when Roy Halladay was sidelined by a shoulder injury, was fortunate to leave after five innings with a 3-1 lead. He gave up six hits and three walks while finding trouble often.
Brian Duensing (2-1) picked up the victory by stranding runners at first and second in the eighth inning by striking out Ryan Howard on a call the slugger disputed with home plate umpire David Rackley and getting Domonic Brown to pop out.
Pelfrey tossed a season-most 112 pitches with his surgically repaired right elbow. His 6.22 ERA entering the game was still the worst in the majors among pitchers with a qualifying amount of innings, but he has slowly begun to round into form, a little more than a year after the Tommy John ligament replacement procedure.
This was his fourth start this season of six innings or more and three runs or less. He struck out seven, gave up five hits and walked one.
Revere, the second batter of the game, was ruled safe by first base umpire Bruce Dreckman for an infield single after third baseman Jamey Carroll made a lunging stop of a sharp grounder and zipped a throw across the diamond. First baseman Justin Morneau appeared to slap Revere's chest with his glove just after the ball landed in the webbing, but the arguments by Morneau and manager Ron Gardenhire didn't matter.
Revere scored on Brown's sacrifice fly. Then Young followed with a soft single that stretched the lead to 2-0.
Michael Young's two-out double in the fifth interrupted a string of 12 straight batters retired by Pelfrey. Revere's single sank fast enough into shallow center field to keep Thomas from catching it, putting the Phillies up 3-1.
Manager Charlie Manuel expressed concern before the game about his team's struggling hitters, who had a 14-game home run streak end the night before and came into the game just 25th in the majors in runs per game. Young's was the only extra-base hit, and the Phillies had five three-up, three-down innings at the plate.