Jordan Leopold scored his first goal for Pittsburgh at 3:50 of overtime after Atlanta failed three times to hold leads, and the Penguins bounced back from one of their worst losses all season to beat the Thrashers 4-3 Saturday.
Malkin had a goal and an assist after sitting out five consecutive games and seven of eight with a bruised right foot. Gonchar, out for four games with strep throat, tied it on a power play with 74 seconds left in regulation and had an assist.
Sidney Crosby had three assists as the Penguins followed up a dismally played 2-0 loss at home to Tampa Bay on Wednesday.
Coach Dan Bylsma held a demanding and unscheduled practice 10 1/2 hours following his team's fourth loss in six games and a postgame meeting, but the Penguins appeared to respond more to the return of Malkin and Gonchar than they did to any punitive measures.
"It's great to have them back," Crosby said. "Obviously for them to miss some time like they did and come back and play the way they did, and make an impact right away, that's huge for us."
Pittsburgh moved ahead of Buffalo and into third place in the Eastern Conference as the Sabres lost to Montreal 3-0. The Penguins and Atlantic Division leader New Jersey have 97 points apiece, but the Devils -- who beat Carolina 4-0 -- own the tiebreaker.
"We didn't have our best game, no, but we made some progress and we got a couple of big guys back in the lineup," Leopold said.
Leopold won it with his eighth goal overall and first since Jan. 31 with Florida, cutting down the right-wing boards before spinning to avoid defenseman Mark Popovic and putting a bad-angle shot past goalie Johan Hedberg.
"I was tired at the end of the shift and actually wanted to get off, and I threw it on the net and I think I surprised them," Leopold said.
Atlanta is a point out of eighth place in the conference with three games remaining: against conference-leading Washington, New Jersey and Pittsburgh. The Thrashers have lost their last eight against the Penguins.
"We had two points and we found a way to squander that," Atlanta defenseman Ron Hainsey said.
Thrashers coach John Anderson didn't like the holding call on Jim Slater that led to Gonchar's 11th goal, on a one-timer from above the circles after Malkin drew multiple defenders to him.
"I feel bad for the guys that played their hearts out. A call like that at the end of the game, you've got to be kidding me," Anderson said.
Atlanta hadn't allowed a power-play goal in nine games until Malkin and Gonchar scored as Pittsburgh went 2 for 5 with the man advantage. Perhaps the Thrashers shouldn't have gotten Malkin upset.
He was visibly angry after getting his No. 71 jersey yanked over his head during a scrap involving multiple players along the boards near the midpoint of the second period, and he yelled over his shoulder toward at least one player as he went to the bench. Not long after, Malkin tied it at 1 on a power play by scoring his 25th goal.
"It was a game you expect when Geno is on his game and dominating play," Bylsma said.
Leopold was traded by Florida on March 1. He hadn't scored in 15 games with Pittsburgh. ... Crosby won the Penguins' MVP award, and F Jordan Staal won the players' player award for his season-long consistency. ... Atlanta rookie Niclas Bergfors has four goals and four assists in five games against Pittsburgh. ... Malkin has six goals and 12 assists in eight games against Atlanta. ... Atlanta played without former Penguins F Colby Armstrong, who served the first game of a two-game suspension.