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.
Williams averaged a career-high 14.9 points per game with the Sixers last season when he was runner-up to Harden for NBA's Sixth Man of the Year Award.
Williams appears bound for another year as a sixth man. Harden is thriving in his new role as a starter.
"It's a lot different," Harden said. "Having the offense run basically through you, it's a lot different, but that's my job now so I've got to get used to it."
Harden said he wasn't focused on his impressive scoring in his first two games.
"I don't even worry about it," he said. "I just go out there and play hard."
The Hawks traded six-time All-Star
Joe Johnson to the
Brooklyn Nets in July for five players and a draft pick. Johnson averaged more than 20 points in five of his seven seasons as Atlanta's top player.
"We're still trying to establish an identity," Hawks coach Larry Drew said. "That may take a little time to do."
Drew said his team struggled in rebounding and on defense, especially in helping stop Harden's drives.
"When he gets the basketball in transition, he's going to get to the basket," Drew said. "It won't be just one guy's responsibility, it will be a team responsibility."
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's 17 free-throw attempts matched Atlanta's total.
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.
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.
"We were just trying to put together as many stops as we could," Williams said. "We battled our way back into the game to even get it to that point."
The Rockets are 2-0, but McHale said the team needs work on closing out wins.
"We need a few days together in the gym where we can slow some things down and figure out how we want to finish games," McHale said.
After a preseason of sampling lineup combinations, Drew had two newcomers --
Devin Harris and
Kyle Korver -- join
Al Horford, Smith and
Jeff Teague. 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.
The Rockets had a 58-36 advantage in rebounds.
"We have some things that we really have to focus in and work on," Drew said. "There were areas in this game where we weren't very good, very polished, particularly on the boards."
Drew said his perimeter players were beaten for too many long rebounds.
"We didn't play well, yet we gave ourselves a chance in fighting back," he said.
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. ... Harden is the first player to score 40 points against Atlanta since
LeBron James had 43 points on March 18, 2011.