Armstrong credited Malkin for setting up the winning goal, which came 3:51 into overtime.
"Malkin read the play well," Armstrong said. "He made a great play to get it to the net. It bounced right to me."
Malkin, 20, snapped out of a slump with a goal and two assists. Sidney Crosby had a goal and an assist, and Marc-Andre Fleury made 20 saves as the Penguins avoided matching their longest losing streak of the season.
"We've been losing a lot of close games," Armstrong said. "To get a win like that against a good team is big. ... We had been in quite a slide."
The Thrashers battled from behind for three ties, including two goals in the third period to force the overtime.
Malkin, the second pick in the 2004 draft, was the first NHL rookie in almost 90 years to score in each of his first six games. The Russian had been held without a goal in four of five games, leading to a meeting with coach Michel Therrien on Friday.
"It's nice when you sit down with a guy and he responds like this," Therrien said, adding Malkin's performance "is a good sign that he understands English, too.
"He played with emotion and really worked hard."
Kari Lehtonen stopped 39 shots as the listless Thrashers were outshot 43-23 and never led. The usually active Ilya Kovalchuk, who averages 4.3 shots per game, had only one shot.
The Southeast Division-leading Thrashers have lost two in a row after winning a franchise record-tying five straight games and seven of eight.
The Thrashers were outshot 16-4 in the opening period, but Pittsburgh's only goal came on Crosby's power-play tally.
"We're all learning together and experiencing a lot of things together for the first time," said Crosby, 19. "Hopefully we can build and grow and improve together and hopefully get some wins."
Atlanta spent most of the first period still stuck in the malaise that marked Thursday night's 8-0 loss at Tampa Bay. The exception to the offensive funk was Shane Hnidy's successful wrist shot from the right circle, a short-handed goal with 1:24 left in the period.
Malkin scored on a pass from Crosby midway through the second period for a 2-1 lead. The Thrashers were further limited on the Penguins' power play as Brad Larsen tried to defend after losing his stick.
A hooking penalty against Mark Recchi late in the second period led to Atlanta's power play that continued into the third period. Marian Hossa got the Thrashers even at 2 just 16 seconds into the period with his 22nd goal, tying Brendan Shanahan of the New York Rangers for the NHL lead.
Pittsburgh pulled ahead 3-2 on Ryan Whitney's fourth goal 7:22 into the period, but Atlanta answered with Niko Kapanen's second goal with 4:48 left in regulation.
Pittsburgh lost five straight from Nov. 4-11. ... Thrashers C Jim Slater was back in the starting lineup after missing four games with a sore foot. ... There were no penalties in the third period following 11 -- seven again Pittsburgh -- in the first two frames.
Copyright by STATS LLC and The Associated Press
Arena: Philips Arena Location: Atlanta, Georgia
Referees: Wes McCauley, Rob Shick Linesmen: Brian Mach, Jean Morin
Attendance: 18,687 (100.8% full)
Team Stat Comparison
Power Play Goals
Power Play Opportunities
Shots on Goal
Sidney Crosby (13)
(Power Play) Assists: Sergei Gonchar, Micki Dupont
Shane Hnidy (2)
(Shorthanded) Assists: J.P. Vigier, Steve Rucchin
Evgeni Malkin (14)
(Power Play) Assists: Sidney Crosby, Sergei Gonchar
Marian Hossa (22)
(Power Play) Assist: Slava Kozlov
Ryan Whitney (4)
Assists: Evgeni Malkin, Erik Christensen
Niko Kapanen (2)
Assists: Slava Kozlov, Glen Metropolit