John LeClair and Sergei Gonchar also scored for the Penguins, who snapped their four-game, road-losing streak and handed the Flyers their fifth straight home loss.
Simon Gagne, Geoff Sanderson, and Frederick Meyer scored for the Flyers, who trailed 3-0 after the first period.
The Penguins are 4-0 against the Flyers this season, outscoring them 20-7.
Whitney threaded a cross-ice pass to LeClair, who flicked the puck past goalie Antero Niittymaki 35 seconds in for the Penguins' first goal on a power play.
Moore made it 2-0 at 4:31 after taking a spectacular centring pass from Crosby, who streaked down the ice, stopped at the circle, spun around and put the puck on Moore's stick.
Whitney scored with nine seconds left in the period, beating Niittymaki high following a scramble.
Gagne's deflection of Joni Pitkanen's long slap shot on a power play got the Flyers on the board at 4:58 of the second period. Crosby answered for the Penguins 49 seconds later with a shot from inside the left circle. Sanderson and Gonchar then traded power-play goals within a span of 2:28, making it 5-2 after two periods.
Meyer's goal came on a scramble during a power play with three seconds left in the game.
Marc-Andre Fleury, who has all four wins against the Flyers this season, made 22 saves - including a brilliant sprawling stop of Gagne's breakaway late in the third period. Niittymaki stopped 29 shots.
Notes: Crosby and Philadelphia C Mike Richards played in their 100th NHL game. ... Flyers D Alexandre Picard, who sustained a concussion at San Jose on Saturday, was scratched. ... Pittsburgh RW Andre Roy was a healthy scratch. ... Crosby has 23 points (13 goals, 10 assists) in 12 career games against the Flyers. ... The last time the Penguins defeated the Flyers at least four times was during the 1992-93 season when they took the season series 5-1-1.