Matt Cullen also scored for the Penguins, who scored three times in a 55-second span in the first period while opening a four-game road trip with their fourth win in the past five. Marc-Andre Fleury stopped 38 shots while making his ninth straight start (6-2-1).
Matt Murray, who led the Penguins to the Stanley Cup last season, was available as Fleury's backup. Murray, recovering from a broken hand, hasn't played this season.
Malkin put the Penguins ahead for good with his milestone goal at 8:33 of the third. Olli Maatta threw the puck toward the net. It bounced off the leg of Philadelphia's Brandon Manning and to the back post, where a wide-open Malkin shot past Neuvirth.
Crosby, who missed the first six games due to a concussion, has four goals and five points in three games since returning.
Trailing 2-0, the Penguins scored three goals during an electrifying 55 seconds late in the first period.
Crosby beat Mason short-side from a bad angle with a top-shelf wrist shot with 4:16 left in the period. Forty-three seconds later, Crosby netted a power-play goal after one-timing a pass from Patric Hornqvist in the slot that whizzed by Mason. Cullen ended the onslaught with a wraparound tally with 3:21 remaining.
The only other time Philadelphia allowed three goals in 55 seconds or less was Nov. 23, 1991, when the Devils tallied three in 42 seconds in the second period of a 5-5 tie. Pittsburgh capitalized on a turnover by Sean Couturier to take a 4-2 lead on Malkin's goal midway through the second period.
The Flyers got back within one goal on Giroux's power-play tally with 6:44 remaining in the period. Radko Gudas made a stellar play to keep the puck in the offensive zone before Wayne Simmonds fed Giroux for a one-timer from the slot that beat Fleury on the glove side.
The play was upheld after a lengthy review to determine whether Philadelphia was offside on the play. The Flyers tied it 2:12 later on Voracek's penalty shot, which was awarded after the Flyers' right wing was pulled down by Brian Dumoulin on a breakaway attempt.
The Flyers were playing their fifth game in eight nights and were on the front end of a back-to-back. ... Giroux extended his points streak to eight straight games. ... Pittsburgh D Kris Letang (upper body) missed his fifth straight game but is close to a return. ... Voracek's penalty shot snapped a string of six straight misses and was Philadelphia's first successful conversion since Matt Read's tally on Nov. 13, 2011. ... The Flyers scored first for just the second time this season and now have three first-period goals on the season.