Jokinen's first goal was his 355th point with the Panthers and his second goal was his 158th. Both records previously belonged to Scott Mellanby.
Gregory Campbell also had two goals for the Panthers, who went 4-0 against the Flyers last season. Richard Zednik and Bryan Allen each had two assists.
Joffrey Lupul, Jeff Carter and Lasse Kukkonen scored for the Flyers, who had their five-game winning streak snapped.
The game began a season-long eight-game road trip for the Flyers.
Florida outshot the Flyers 42-23, including a 14-5 advantage in the second period.
Tomas Vokoun stopped 20 shots for Florida. Martin Biron made 38 saves for the Flyers.