Harden, traded to the Rockets from Oklahoma City on Saturday, topped 30 points for the second time in his first week with his new team.
Jeremy Lin had 21 points, 10 rebounds and seven assists and Marcus Morris had 17 points for Houston.
Rockets center Omer Asik had a career-high 19 rebounds but did not score, missing seven shots from the field.
Lou Williams led the Hawks with 22 points in his Atlanta debut. Josh Smith had 18 points and 10 rebounds.
With the game tied 92-92, Harden had consecutive baskets, including a three-point play, to give Houston the lead for good. Chandler Parson’s 3-pointer with 1:55 remaining pushed the lead to 100-94.
Harden was 14 of 19 from the field and 15 of 17 from the free throw line.
Harden, who signed a five-year, $80 million contract extension with Houston following the trade, had 37 points, 12 assists and six rebounds in a 105-96 win at Detroit in his debut on Wednesday night.
Rockets coach Kevin McHale said before Friday night’s game he was impressed with Harden’s basketball smarts, enabling him to make a quick adjustment to his new team.
Houston led after each of the first three periods. The Rockets took a 68-52 lead in the third before Atlanta cut the deficit to 81-74 at the end of the quarter.
A basket by Smith with 7:12 remaining gave Atlanta an 88-87 lead, its first since the opening period.
The Hawks have a new-look roster after trading Joe Johnson and Marvin Williams.
After a preseason of sampling lineup combinations, Hawks coach Larry Drew had two newcomers — Devin Harris and Kyle Korver — join Al Horford, Smith and Jeff Teague. About 90 minutes before the game, Drew said he had “a little indecision” about Harris starting at shooting guard as the coach worried about the defensive matchup with Harden, who at 6-foot-5 is at least 3 inches taller than Harris.
DeShawn Stevenson, who could match Harden’s height — and at least come close to matching Harden’s beard — became an important player off the bench for Atlanta.
Stevenson had 12 points on four 3-pointers, including one at the buzzer to end the first half.
Teague had 14 points and seven assists and Horford had 14 points.
Notes: Houston F Patrick Patterson started after missing the opener with a strained left quad. C Greg Smith (strained left foot) did not play. ... Harden’s previous career high was 40 points against the Suns on April 18. ... Hawks C Johan Petro was inactive. ... Stevenson fouled out in the final minute.