Malkin deked to the left and brought the puck back to the right to put a backhanded shot past Roberto Luongo. Ryan Kesler had a chance to prolong the shootout for the Canucks, but Penguins goalie Marc-Andre Fleury stopped his attempt.
"I always liked [the shootout], but I didn't score [in previous attempts]," Malkin said. "Last year, I scored a couple goals, and the year before I scored lots of goals. Now, I know what's going on and I know the goalies and I just did my move and scored."
"When Malkin came down, I wasn't sure what he was going to do," Luongo said. "Unfortunately, I bit on the fake and he went backhand. So I wish I would've been a bit more patient and got that one."
The Penguins remained unbeaten at home through five games.
Brandon Sutter had an opportunity to give Pittsburgh the lead with 1:24 left in the third period when he was awarded a penalty shot, but Luongo made a glove save to keep the game tied 3-3.
The Canucks took a brief lead in the third period when Zack Kassian deflected David Booth's point shot past Fleury to put the Canucks up 3-2 with 7:10 left. But Chris Kunitz found Olli Maatta charging toward the Vancouver net 22 seconds later and the 19-year-old defenseman sent the puck behind Luongo for his first NHL goal, tying the game.
Canucks coach John Tortorella said he was disappointed with the defensive lapse leading to Maatta's goal but was pleased with his team's performance.
"[Kesler] made a big hit, but the puck was available and they ended up with an odd-man rush," Tortorella said. "But you know what? We just kept on playing and found a way to get a point, and you want two, but I thought we played, for the most part, a number of minutes really well tonight."
Vancouver's top-ranked penalty killing unit (92.3 percent entering Saturday) shut down two Pittsburgh chances in the first period, but the Penguins took advantage of their third opportunity when Kunitz gave Pittsburgh a 2-1 lead 7:56 into the second.
Crosby passed the puck behind the net to Malkin, who sent it in front to Kunitz. He slapped the puck inside the left post for his fourth goal of the season.
Crosby added a goal and a second assist to give him a League-best 17 points, six more than St. Louis Blues forward Alexander Steen and Vancouver's Henrik Sedin, who assisted on Alex Edler's first-period goal. Crosby's first-period goal, which tied the game 1-1, gave him seven on the season, tying him for the League lead with Steen and San Jose Sharks rookie Tomas Hertl.
On the Pittsburgh captain's tying goal, Pascal Dupuis' long shot deflected off Luongo's glove to Crosby, who took two whacks at the puck to send it into the back of the net.
The goal extended Crosby's point streak to eight games, the longest of his career to start a season.
"I think as a group, we're finding ways to win," Crosby said. "Today wasn't our best game, but [Fleury] shut the door when we needed him to and we found some ways to get back in the game and get a great goal from [Malkin] in the shootout.
"We still want to get better."
Brad Richardson tied the game 2-2 with 7:16 to play in the second. On an odd-man rush, Dale Weise carried the puck through the neutral zone and found Kevin Bieksa, leaving Richardson open. Bieksa slid a pass to Richardson, who one-timed a shot past a diving Fleury.
Canucks captain Henrik Sedin said he thought Vancouver controlled much of the game but allowed Pittsburgh to hang around.
"For half the game, I thought we played great," Sedin said. "The second half, I thought we gave up a little too many scoring chances. They came out on 3-on-2s, 2-on-1s a few times and [Luongo] made some big saves for us.
"But for half the game we were all over them."
The Penguins registered five shots in the first period but had several scoring chances; three shots rang off the goal cage.
Pittsburgh appeared to take a 1-0 lead when Chris Conner sent a shot off the post behind Luongo, causing the goal horn to blare and the linesman to point at the net. However, play continued while the Consol Energy Center crowd voiced its displeasure.
Matt Niskanen and Maatta also hit posts, while another bout of bad luck led to Vancouver's first goal.
Edler, in his first game back after serving a three-game suspension for a check to the head of Hertl on Oct. 10, attempted to send the puck deep into the Penguins zone by shooting it from center ice. The puck hit Fleury in the chest, popped into the air, went behind him and trickled over the goal line before he could lunge back to stop it, giving the Canucks a 1-0 lead with 6:11 left in the first.
Fleury rebounded nicely after the goal and stopped 36 of the 39 shots he faced.
"It was unfortunate, on the first goal he gets a shot up near his mask and he doesn't know where it is," Penguins coach Dan Bylsma said. "He'd like to forget about the first one and I think he's able to with how he played and shootouts have been a strong suit and it was again for us."