Jefferson matched a career high with 22 rebounds, but couldn't keep the Timberwolves from losing for the fifth time in six games.
The Rockets took control late in the third quarter as the Timberwolves went cold from the field.
Minnesota led 69-66 before Alston sank two 3-pointers in the last 90 seconds of the third quarter to launch a 17-2 Houston run. Shane Battier added another 3 and Yao scored inside in the first minute of the fourth to put the Rockets up 83-71.
The Wolves missed 10 of 11 shots over the decisive 7½-minute span. It was an encouraging stretch for the Rockets, who've struggled to put teams away all season, mostly due to stretches of lackluster defense.
"If we play with that type of energy, scrambling, helping each other on defense, covering for one another," McGrady said, "that's what we do, that's who we are."
Jefferson's hook shot with 7:35 left in the game cut the deficit to 87-75, but Carl Landry dunked and McGrady sank a 3-pointer on the Rockets' next two possessions.
Minnesota shot 39.8 percent from the field (35-of-88) and got outrebounded 51-39.
"The defense still needs improvement, but overall it was good," Alston said. "We turned it up. It wasn't a good start in the first quarter, we were giving them everything, points in the paint, 3-point shots. But as the game progressed, we gradually got better defensively and we were able to put them away."
Houston led 8-0 in the opening minutes, but the Timberwolves answered with a 16-0 burst, capped by a pair of 3-pointers by Randy Foye.
The Rockets missed their first 11 shots inside 3-point range. Coach Rick Adelman finally called timeout and inserted Artest to replace Battier, the starting forward. McGrady immediately hit a jumper from the free-throw line to end a five-minute Houston scoring drought.
But Jefferson scored 17 points on 8-of-12 shooting with eight rebounds in the first quarter, dominating Yao, who started 0-for-4 from the field. Jefferson seemed to have Yao scouted well, drawing him away from the basket, then using his quickness to duck around him.
"I knew I had an advantage with Yao," Jefferson said. "I wanted to get him on the move and I was able to hit my jumpers."
Adelman replaced Yao with shot-blocking specialist Dikembe Mutombo, but Minnesota opened the second quarter with a 7-0 run to lead 34-20. Artest scored, but Foye hit another 3-pointer with 8:45 left in the half to put the Wolves up 37-22, their biggest lead of the game.
"We were moving the ball and attacking them in the first half," Jefferson said. "Then, we got away from it."
Yao returned and slipped inside for consecutive dunks to get the Rockets back on track. McGrady sank a straight-on 3-pointer with 5:21 left in the half to cut the deficit to 39-35.
The Rockets fell behind by eight before riding an 11-2 run to a 49-48 lead. The game was tied at 50 at the break.
Jefferson scored 21 points and grabbed 13 rebounds in the first half for his fifth consecutive double-double.
Early in the third quarter, Jefferson blocked Yao on a left-handed layup try and Yao grabbed his left shoulder in pain. He left briefly, returned with 7:34 left in the quarter and flipped in a hook a minute later to tie it at 60.
"I knew it wasn't that serious," Yao said. "But at the time, my forearm felt like it was getting burned."
- Houston guard Aaron Brooks, who missed Wednesday's loss in Memphis with flulike symptoms, played nine minutes.
- The Rockets are 11-1 this season at home when they score 100 points or more.
- Minnesota F Craig Smith sat out for the second straight game with bruised ribs. Minnesota coach Kevin McHale said Smith would not return before the All-Star break.