Portland had won five in a row, but ran out of steam in the final effort of a four-game road trip. It was only the fifth loss of the season for the Trail Blazers and just their third setback on the road.
Minnesota built a 26-point halftime lead while climbing back to the .500 mark.
Pekovic had 30 points and nine rebounds while Love narrowly missed a triple-double with his 29 points, 15 rebounds and nine assists.
Kevin Martin came off the bench to score 22 points for the Timberwolves.
Portland's Damian Lillard equaled his season's best for the second straight night with 36 points. He also reached that total on Tuesday in a win over Cleveland.
The game was billed as a showdown between Love and Portland's LaMarcus Aldridge, two of the game's top power forwards. Aldridge had 15 points and 14 rebounds.