The Rockets lost at home for just the fourth time this season, falling to a team that shot 55 percent from the field. Houston was coming off a win Wednesday over Oklahoma City, the top team in the Western Conference.
Love scored 33 points and grabbed 17 rebounds. Pekovic poured in a career-best 30 points and seized 12 boards.
Minnesota, which has won two in a row after four straight losses, took a 14-point lead into the fourth quarter.
Chandler Parsons led Houston with 18 points. The Rockets made half their 20 attempts from beyond the 3-point arc, but they made only eight free throws while Minnesota hit 20.