Kovalchuk scored with a little over a minute left in regulation and Rich Peverley got the winning goal in a shootout to lift the Atlanta Thrashers to a 2-1 win over the slumping Florida Panthers on Saturday night.
Johan Hedberg stopped 30 shots for the Thrashers, winners of five of their last six.
"To get that final goal in the last minute was huge," Peverley said. "Coming out of here with two points is really big."
Stephen Weiss scored the lone goal in regulation for the Panthers, who have lost seven of their last eight.
Vokoun made 36 saves in his first start since sustaining a head injury during Florida's loss to the Thrashers on Monday. He was struck in the head when teammate Keith Ballard swung his stick in a fit of frustration after an Atlanta goal. Vokoun needed stitches in his left ear and was sidelined for two games.
"I thought Vokoun played a great game, considering the circumstances," Florida coach Pete DeBoer said. "He really battled hard for us."
Vokoun held the shutout until 1:04 remained in regulation, when Kovalchuk tied it at 1 with a slap shot. Maxim Afinogenov and Tobias Enstrom each had assists on the goal, Kovalchuk's 16th of the season.
"They played so solid defensively, they really kept us on the outside and Vokoun was solid in net," Hedberg said. "We had to work hard to get that goal at the end."
It was the second consecutive home game in which Florida has blown a lead late in the third period. T.J. Galiardi and Matt Duchene both scored for Colorado with less then a minute left in regulation to force overtime on Wednesday night. The Panthers eventually beat Colorado 6-5 in a shootout.
Florida's loss to Atlanta on Monday also came late in the game, when Afinogenov scored with six seconds remaining in the third period to give the Thrashers a 4-3 win.
Kovalchuk also netted a goal in the first round of the shootout, but Steve Reinprecht got a goal for Florida in the third round to keep it alive.
Weiss' goal, his 13th of the season and sixth in four games, came on the power play at 2:36 of the third. He tipped in Dmitry Kulikov's shot from the blue line, sending the puck under Hedberg's pads to give the Panthers a 1-0 lead.
"It just wasn't meant to be tonight," DeBoer said. "We live to fight another day. I told the guys after the game that we play like that, we're going to win a lot more than we lose."
Vokoun wore a skull wrap to hold down his ear and extra padding around the injury. Vokoun's injured ear looked bruised and swollen after the morning skate. ... After hosting Edmonton on Monday, Florida begins a four-game road trip.