That left reserve Greg Smith free to make some big plays.
Harden scored 21 points and Smith added 20 to help the Rockets to a 101-89 win over the Celtics.
"They were going to overcompensate," Houston coach Kevin McHale said of Boston's defense on Harden and Lin. "So if you roll behind there is going to be some openings, and Greg did a great job of presenting himself, catching and finishing around the basket."
Smith, a second-year player who fell one point short of his season high, hit 8-of-9 shots and also grabbed six rebounds and had three blocks.
"I was in the right spots at the right time," Smith said. "I knew if they passed the ball to me, the best thing I could do is finish it."
Harden had 10 points, four assists, two rebounds and a steal in the third quarter as Houston built its lead.
The Rockets used a 9-2 run capped by a 3-pointer by Harden to open the period and go on top 52-47. They never trailed after that and cruised to the victory.
"In the third quarter we didn't stop them," Boston's Kevin Garnett said. "We were trying to create some defensive consistency and we just weren't able to do that."
Paul Pierce led Boston with 18 points after scoring a season-high 34 in the Celtics' double-overtime win against Dallas on Wednesday.
The Celtics haven't had a great start to the season, but thought they had turned a corner recently after winning two in a row.
"We took a step back tonight," Pierce said. "We were playing every other quarter. We've got to come out with the right mindset to be consistent."
Harden, who had scored 30 or more in his last two games, got off to a slow start before heating up in the third quarter. Chandler Parsons added 15 points and Omer Asik had nine points and 10 rebounds for the Rockets, who won their second straight.
Rajon Rondo had 15 points, 13 assists and four steals for Boston, but also committed seven turnovers. Garnett chipped in 14 points for the Celtics, who shot 40 percent.
"We had some runs, but I never felt like we were going to win the game tonight," Boston coach Doc Rivers said. "I don't know why and I'm disappointed in the loss."
Rondo tried to swipe the ball from Harden as he dribbled near the 3-point line with less than 5 minutes remaining. But he missed the ball and fell to his hands and knees as Harden pulled up and swished a 3 to extend Houston's lead to 91-83.
Another nifty play came about 1 1/2 minutes later when Parsons stole a pass by Rondo. Parsons dribbled down into the lane before kicking it out to Toney Douglas for a 3-pointer. Douglas added a three-point play a few seconds later after a missed 3-pointer by Pierce to put Houston up 99-85.
The Celtics had cut the lead to five with a 6-2 run before Carlos Delfino hit a 3 for Houston with about 8 minutes left.
Courtney Lee grabbed a steal on a bad pass by Delfino soon after that, and was dribbling down the court on a fast break when play was stopped by an inadvertent whistle. Rivers was not happy with the miscue and walked several steps onto the court while yelling as the ball was reset.
Houston was up by nine points until Rondo made two free throws followed by a put-back dunk by Jared Sullinger to cut the lead to 75-70 entering the last quarter.
Houston led by as many as 13 in the first quarter, and was up by eight before Boston used a 13-3 run to take a 34-32 lead about 6 minutes before halftime. Jason Terry tied the game with a 3-pointer in that run, and Rondo gave Boston its first lead of the game with a layup.
The Celtics had built their lead to seven points before Houston ended the half with a 9-5 spurt to get within 45-43 at halftime.
Lee, Garnett and Rivers approached McHale after the game to express their condolences on the death of his 23-year-old daughter Alexandra "Sasha" McHale, who died Nov. 24 of complications from Lupus. McHale became very emotional during the exchange.
"I got to go over and give him a hug and talk for a little bit," Lee said. "I saw the tears rolling down his face and it was definitely an emotional time for me."
Houston begins a two-game road trip to Toronto and New York on Sunday. ... Lee, who played for Houston last season, finished with eight points and three rebounds.