McGrady, wearing a bandage on his left shoulder after spraining it late in Monday night's win over Sacramento, was 4-for-15 from the field after three quarters. He made three straight jumpers in a 2-minute span in the last quarter as the Rockets opened a double-digit lead and finally put the Timberwolves away.
The Rockets outrebounded the Wolves 58-38 and scored 14 second-chance points to win for the 19th time in their last 21 home games.
Al Jefferson had 21 and 10 rebounds for Minnesota, which had won four of its last six games.
The Rockets looked sluggish most of the night, going 4-of-19 from 3-point range, committing 14 turnovers and never leading by more than 12. They play seven of their final 10 games on the road, starting Sunday at San Antonio.
Kirk Snyder, acquired from Houston in a trade on Feb. 21, had seven points and four assists in the first quarter to keep the Wolves close. He finished a fast break with a dunk, but Rafer Alston sank a 3-pointer in the final seconds of the quarter to give Houston a 24-23 lead.
The Rockets built an eight-point lead in the second quarter, but the Timberwolves stayed close behind Jefferson and Ryan Gomes, who scored 10 points apiece in the first half. Gomes finished with 17.
McGrady aggravated his shoulder injury on a drive into Marko Jaric just before halftime. He winced as he walked to the free-throw line, but both shots to put the Rockets up 46-40. Houston rebuilt its eight-point lead early in the third quarter. Gomes made a 3-pointer and Jefferson dunked over Dikembe Mutombo to cut it to 53-50.
Scola had a putback and converted a three-point play to push the lead back to eight. He had a steal later in the quarter that led to an easy layup for Alston.
The Rockets outrebounded Minnesota 46-31 through three quarters and led 69-60.
The Wolves opened the final quarter with a 12-5 run, spurred by three straight baskets by Rashad McCants. Bobby Jackson and McGrady answered with consecutive baskets to push the lead to 78-72. Jackson tipped in McGrady' miss to put Houston up by 12 with 4:15 left.
The Rockets have won 29 of their last 33 games.
Notes: At halftime, the Rockets honored Mutombo with a video tribute. Team owner Les Alexander presented Mutombo with a $500,000 check for the hospital that Mutombo built in the Democratic Republic of Congo. NBA commissioner David Stern was on hand for the ceremony. Yao Ming, on crutches after breaking a bone in his left foot in late February, also attended. ... Former president George H.W. Bush had a courtside seat next to Houston Astros owner Drayton McLane. ... Snyder had 12 points and six assists for Minnesota. ... McCants scored 16 points.