The historic blast came in the seventh inning off Tigers left-handed reliever Daniel Schlereth. The 40-year-old became the eighth player in baseball history to reach the milestone, and the first since Yankees third baseman Alex Rodriguez last season.
Thome entered play with 598 career homers, and hit his first of the contest -- a two-run blast to left -- in the sixth inning off Detroit starter Rick Porcello.
"I envisioned doing this in Minnesota, amongst the home fans. But to do it anywhere is great," said Thome. "To do it in a Twins uni is just very cool. In a visiting park, they give you a standing ovation is just cool. To watch them stand up and cheer is very special. (It's) something I'll never forget."
Ben Revere added two hits and two RBI for the Twins, who won for just the second time in their last 10 games.
Victor Martinez hit a two-run home run, Ryan Raburn added a solo homer and Alex Avila finished 3-for-4 and a home run short of the cycle for the Tigers, who have lost two in a row following a three-game win streak.
Delmon Young, who was acquired by Detroit prior to the game from Minnesota for pitcher Cole Nelson and a player to be named later, also went deep in the setback.
It didn't help Porcello (11-8), who was tagged in defeat for nine hits and six runs -- four earned -- over six full frames.
In the Minnesota seventh, Trevor Plouffe worked a leadoff walk, stole second and moved to third on a wild pitch. Justin Morneau walked and Jason Kubel fanned, setting the stage for Thome, who struck an opposite-field, three-run shot which barely cleared the wall in left field to give the Twins a 9-5 advantage.
As Thome approached home plate, several members of his family raced onto the field and anticipated his arrival steps ahead of his teammates.
"To share it at home plate with my teammates and my family...it was just a very special night," Thome added. "They were really grinding it out, traveling with the team. School starts in a week. My dad's here, my sister's here. With all the injuried and hype, it was just a sigh of relief to get it over with. "
Raburn cut the Tigers deficit to three by greeting Alex Burnett with a homer to left, but after a Miguel Cabrera single, Glen Perkins got the call and prevented further damage. He also recorded the first two outs in the eighth before giving way to Matt Capps.
Nathan retired the side in order in Detroit's final turn.
Young hit a two-out solo shot in the home first which gave the Tigers -- his new club -- a 1-0 lead over his old mates.
Minnesota picked up three runs in the third thanks to a costly error. After Matt Tolbert reached on a bunt single, Raburn's wild throw on a Tsuyoshi Nishioka grounder put runners on the corners. Revere then posted an RBI groundout, Plouffe hit a run-scoring double and Morneau followed two batters later with another RBI two-bagger.
After Cabrera singled, Martinez slugged a two-out homer in the home half for a 3-3 game.
Kubel led off the sixth with a base hit and Thome racked up No. 599 with his two-run blast to left-center. Danny Valencia followed with a walk and scored when a Revere hit rolled all the way to the wall in center, but Minnesota's speedy center fielder was thrown out at home trying to make it an inside-the- park homer. Nonetheless, the visitors led 6-3.
The Tigers came back with two in their turn on a triple from Avila and a Wilson Betemit sacrifice fly.