The win was San Antonio's sixth in its last seven games and 10th in a row over the T'Wolves.
Al Jefferson scored 20 and Kevin Love 18 for Minnesota.
San Antonio put together a pair of 6-0 runs in the second quarter to break away and take a 66-52 halftime lead.
Love hit a pair of free throws in the third quarter that narrowed the gap to 76-67 but the Spurs responded with 10 unanswered points and led 89-73 at the start of the fourth quarter.
Richard Jefferson nailed a pair of 3-pointers to begin the fourth quarter to extend the lead.