Lin was noticeably absent from the spotlight at the end of the actual game, following another poor shooting night.
Harden scored 28 points, Patrick Patterson added 20 and the Rockets snapped a three-game losing streak by beating the Bulls on Wednesday night.
"Defensively, we played pretty well," Harden said. "That's what kept us in the game. Offensively, at times, we struggled, but our defense really locked in at key moments down the stretch."
Toney Douglas, who replaced Lin late in the game, swished a 3-pointer and sank two free throws in the final 1:11 as Houston won for the 33rd consecutive time when holding its opponent below 90 points, the NBA's longest current streak.
Lin went 2 for 9 and scored only four points in his final game before facing his former team when the New York Knicks on Friday. He came in shooting 34 percent from the field and 24 percent from 3-point range.
"I'm happy because we had lost three in a row and needed a win," Lin said. "Me, in terms of how I'm playing, I'm a little disappointed in myself. It's just a matter of continuing to fight, continuing to get better."
Lin went 5 for 15 in a loss in Utah on Monday night, and he was 15 for 50 overall from the field over his previous five games. He was getting the shots he likes on Wednesday night, they just weren't falling.
"It was just one of those things where I haven't had the rhythm I've wanted to have," Lin said. "That'll come over time."
Nate Robinson scored 21 off the bench, Luol Deng added 19 and Carlos Boozer had 13 points and 15 rebounds for the Bulls, who've lost three in a row for the first time in Tom Thibodeau's three seasons as coach.
The Bulls forced 23 Houston turnovers and outrebounded the Rockets 48-45, but went 2 for 16 from 3-point range and struggled to find any offensive flow.
"There are a lot of things we need to do," Deng said. "We've just got to put a whole 48 minutes together, just got to stay mentally strong. We've got to get a win and get it rolling again."
Robinson had the highlight of the game, spinning around Lin in midair for a layup with five minutes left to put the Bulls up 81-79. Robinson swished a 3-pointer on Chicago's next possession, and Lin went to the bench.
Douglas guarded Robinson after that, and Robinson only scored two points the rest of the way.
"I felt like Toney gave us our best chance to win," Houston interim coach Kelvin Sampson said. "He was a better matchup with Nate."
The Bulls' offense bogged down at the end, and Douglas' 3-pointer with 1:11 remaining put Houston up 86-84. The Rockets acquired Douglas in a trade that sent Marcus Camby to New York in July.
"He works so hard," Harden said of Douglas. "He had the courage to step into that shot and shoot it."
The Bulls got two offensive rebounds, but Robinson flipped a wild pass from under the basket that hit Deng's hands and went out of bounds.
Douglas sank two free throws and former Bulls center Omer Asik blocked Noah on a drive.
Chicago has lost three in a row for the first time since a 10-game slide between Feb. 27 and March 19, 2010. The Bulls held a team under 100 points for the first time in five games, but couldn't get the stops when they absolutely needed them.
"Our defense is not what it used to be," Noah said. "It's not what it was last year, that's for sure. We have to do better. Losing three in a row is unacceptable. We're better than that."
The Bulls led the league in scoring defense last season (88.2 points per game), and Thibodeau is seeing inconsistency this year.
"The big thing on defense is everyone has responsibility," he said. "We have to stay disciplined and we have to stay attached and we can't make things up. The fourth quarter is different. Your intensity is higher and you have to stay disciplined."
Chandler Parsons had 18 points and a career-high 13 rebounds for Houston. ... Harden tied a career high with five steals. ... The Rockets have won the last two meetings with Chicago after losing the previous five. ... Boozer has three double-doubles in his last four games.