Harden scored 28 points and Dwight Howard had 15 points and 20 rebounds, leading the balanced Rockets to a 111-98 victory over the Spurs on Wednesday.
Each of Houston's starters scored in double figures as the Rockets improved to 2-0 against the Spurs this season, with both victories coming on the road. They also moved within 3 1/2 games of San Antonio (22-7) for the lead the Southwest Division.
"I think we can be very good," Houston forward Chandler Parsons said. "It's obviously a process, and we're getting better every single day. But when we defend like that, rebound well and get out in transition, we're tough to beat."
Harden scored 31 points in Houston's 112-106 victory against San Antonio on Nov. 30. The Rockets have won their last three against the Spurs dating to last season and are averaging 108.8 points over the last six games in the series.
"We just didn't give very good performances," Spurs coach Gregg Popovich said. "You can live with that from time to time. Nobody's going to play perfect every night. But you can't combine poor performances with a lack of physicality and a lack of discipline. They whipped us. They whipped us good. That's an embarrassing loss."
The Spurs have dropped two of three and split their last six games. They are just 3-6 over the last month against teams with a record above .500.
"We didn't play well," Parker said. "Move on to the next one, it's the NBA."
San Antonio never recovered after Houston raced to a 27-9 lead. The Spurs were unable to stop Parsons' long shots, Harden's drives, Howard in the paint or Jones on the boards for follow ups.
"Our guys really came out on fire," Rockets coach Kevin McHale said. "They were excited to play. Really moved the ball; attacked. Terrence had great energy. He was running and helping the defense. We really set the tone early and rode that the entire game."
Houston led 40-25 after one. It was the most points allowed by the Spurs in the opening period this season, and tied for the most in any quarter. Oklahoma City scored 40 points in the second quarter of its 13-point victory Dec. 21 in San Antonio.
"The first quarter was embarrassing," Ginobili said. "They picked us apart. We were not as aggressive as they were, not as sharp as they were and they scored 40. So it's the second time that happened and that's way too many."
Ginobili slammed the scorer's table with his right palm during a timeout with Houston leading 27-11.
After trailing by 18 points in the first half, San Antonio had a couple solid stretches in the second half but couldn't make the plays it needed to complete the rallies.
"We toughened up," Parsons said. "We understand that this is a great team playing on their floor, and we have to get some big stops. Everyone collectively bought into that, we got some huge stops and we didn't stop running, either."
Leonard's three-point play on Howard's fourth foul pulled San Antonio to 71-64 with 4:47 left in the third. The Spurs closed to 73-71 before Harden and Lin began draining long jumpers to help the Rockets pull away again.
Harden closed out the victory, scoring 16 points in the final quarter after missing the previous two games with an ankle injury. His second 3 of the game made it 100-90 with 5 minutes remaining.
"No, I just was getting the feel the first three quarters of who's making shots," Harden said when asked if he was waiting on the fourth quarter. "I missed two games. I wanted to get a feel for who was playing well. Coming into the game, I wanted to keep them involved and keep them going and try to get mine towards the end."
NOTES: Rockets G Patrick Beverley (right hand) and C Omer Asik (thigh contusion) missed the game. ... Academy Award winner Tommy Lee Jones sat courtside, a row in front of David Robinson's customary seats. The actor laughed and applauded when The Coyote, the Spurs' mascot, snuck beside him disguised as a Christmas tree. ... Terrence Jones pushed Matt Bonner after the Spurs' reserve forward wrapped up Howard high after the Rockets star grabbed his third offensive rebound on one possession. Duncan stepped between, putting his hand in Jones' chest and pushing him away before officials broke up the gathering. ... While the Rockets got smatterings of cheers throughout the game, Howard was lustily booed whenever he attempted a free throw or entered the game.