Claude Giroux scored for the Flyers in the first game for both teams since the end of the 113-day NHL lockout.
Chris Kunitz added an empty-netter in the final seconds for the Penguins.
About 20,000 fans filled the Wells Fargo Center and they were welcomed back and thanked by the team in videotaped messages throughout the game.
The rivalry started early in this abbreviated season. The Flyers eliminated the Penguins in six games last season in an Eastern Conference first-round playoff series. Counting the 2012 regular-season finale, the Penguins have played the Flyers eight straight games.