Pekovic hit 9-of-15 shots from the field and 7-of-8 free throws to lead the T'Wolves to their first win over the Hawks since 2006.
Andrei Kirilenko also had a hot hand, hitting 7-of-11 shots for 21 points and six boards. Derrick Williams added 17, and Minnesota scored 20 points as a team from the free throw line.
Minnesota led 58-42 at the half and outscored the Hawks in each quarter except the fourth. The Hawks cut the lead to 102-101 with 1:07 to play but Pekovic responded with a jump shot with 52 seconds to play that proved to the decisive score.