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.
Jokinen, who went scoreless on a recent three-game road trip, made it 1-0 2:35 into the game. He grabbed a long rebound between the faceoff circles and fired a wrist shot over the left glove of Biron.
Jokinen made it 2-0 at 8:56 of the first on a power-play goal. He took a pass from Zednik and sent a wrist shot that beat Biron.
After the Flyers tied the game with goals on their first two shots of the second period, Campbell gave Florida the lead again at 14:16.
His long-distance wrist shot through the legs of defenceman Jason Smith handcuffed Biron and trickled under his blocker.
Campbell made it 4-2 at 1:59 of the third when he stole the puck in front of the Flyers' net and sent a backhand off the post.
Kukkonen cut the lead to one at 12:46 when his backhand pass from behind the net went off the stick of defenceman Ruslan Salei and then off the stick of Vokoun.
Notes:The Flyers had not allowed more than one goal in any of their previous 15 periods. ... Florida LW Stefan Meyer made his NHL debut. ... Flyers LW Ben Eager returned after missing three games with dizziness. ... LW David Booth (neck), D Mike Van Ryn (knee) and C Rostislav Olesz (wrist) missed the game for Florida because of injuries.