The Twins announced the move on Monday. Thomas gives manager Ron Gardenhire another player who can play center field while Wilkin Ramirez is on the disabled list with a concussion.
Rookie Aaron Hicks, who made the jump from Double-A to the majors this season, has played in 50 of the team's 54 games.
Thomas hit .296 with nine home runs and 25 RBIs for Rochester. The 28-year-old played in 12 games with the Twins last season.
To make room for Thomas on the 40-man roster, the Twins designated left-hander Tyler Robertson for release or assignment.