Minnesota has won two of its last three games to reach 20 victories for the season.
Pekovic scored 27 points and claimed 18 rebounds, pushing the Timberwolves to a 13-point cushion early in the final period.
Derrick Williams contributed 17 points for Minnesota and Andrei Kirilenko had 15.
Philadelphia, which has lost three in a row, was led by 17 points from Evan Turner.
Neither side could shoot better than 40 percent from the field and both missed 11 free throws.