Kovalev took the reins of the league's top-ranked power play, netting the game's first goal and collecting an assist with a man advantage during a 27-second span of the second period to give the Penguins a 2-0 lead.
Jan Hrdina had a goal and two assists and Ville Nieminen added a goal and an assist as the Penguins improved to 6-1-0 in their last seven visits to HSBC Arena. The NHL's leading scorer, Lemieux missed his first game of the season after being sidelined for 58 contests during the 2001-02 campaign.
Penguins goaltender Johan Hedberg made 43 saves, including 17 in each of the final two periods.
Buffalo captain Stu Barnes spoiled Hedberg's shutout attempt midway through the third period, but the Sabres still have won just once in 16 games (1-11-3-1).