"I didn't mind him being out, I'm not going to lie to you," Nabokov said. "I wish him well. He's a good person."
Patrick Marleau had two goals and an assist to help the Sharks beat Atlanta 4-3 on Saturday night, the Thrashers' third straight loss.
Kovalchuk did not return after taking a puck off his foot midway through the first period. The Thrashers' captain, who began the game tied for the NHL lead with nine goals, skated off the ice at the 8:43 mark of the first.
"He's going to the doctor, probably Monday morning, have it scanned and X-rayed to figure out what it is," Atlanta coach John Anderson said.
Anderson added that swelling in Kovalchuk's foot is expected to be too substantial for him to see a team physician Sunday.
Marleau's eighth goal, coming on a wrister against Johan Hedberg, made it 3-0 in the first minute of the second.
After Todd White's unassisted slap shot cut the lead to 3-1 at the 3:53 mark of the second, Marleau's ninth goal over 6 minutes later on a power play put the Sharks up 4-1.
With 19:20 remaining, rookie Evander Kane scored his third goal on a wrister from the slot to cut San Jose's lead to 4-3.
Heatley made it 2-0 with a wrister on the power play 13:53 into the first. The goal was his seventh of the season.
Anderson pulled Hedberg, who dropped to 1-1 after stopping eight of 12 shots. Ondrej Pavelec stopped all 12 shots he faced.
"Very disappointing to lose the last two games," Hedberg said. "We came back from a great trip and wanted to get everything moving. It's a long season, and we need to learn from this and move on from here."
Nabokov improved to 6-3 after stopping 24 of 27 shots. Without Kovalchuk to fuel an Atlanta power play that led the NHL with a 28.6 percentage, Nabokov had less to worry about.
"We knew their power play was good," Nabokov said. "When they their second goal [at even strength], they started believing in themselves."
Heatley played to the usual boos at Philips Arena. It's been that way since the 2002 Calder Trophy winner asked for a trade to Ottawa following the 2003 car accident that killed his Dan Snyder.
Heatley was driving while Snyder, his friend and teammate, rode in the front passenger seat.
But since first returning to face the Thrashers in 2005 with Ottawa, Heatley has chosen to speak only with reporters during post-game and to keep the topic on hockey.
"You always want to score against your old team," Heatley said. "We got off to a good start. We kind of let them back in the game. We weathered the storm."
Rich Peverley's fifth goal for Atlanta cut the lead to 4-2 on the power play 17:55 into the second. ... After killing the 12 penalties they faced in the last two games and 22 of 23 over the last four, the Thrashers gave up a pair of power play goals in the four penalties they faced. ... San Jose improved to 9-1-2 in the series.