Bouwmeester tied the game with 3.7 seconds left in regulation and Jokinen scored the winner in overtime to lift the Florida Panthers to a 2-1 win over Philadelphia on Saturday night.
The Flyers matched a franchise record with 10 straight losses and All-Star center Mike Richards, who leads the team with 66 points, will miss three weeks with a torn left hamstring.
"There's no sense waving a white flag right now," general manager Paul Holmgren said.
No, but surely this loss crushed the Flyers more than any other of the previous nine.
The sold-out Flyers crowd was going wild in anticipation of the winless skid finally coming to an end, and Daniel Briere's second period goal was only seconds away from being the winner.
Instead, the puck appeared to tick off Bouwmeester in front of the crease and past Antero Niittymaki, stunning the Flyers in the final ticks and silencing the crowd.
"The way things have been going around here the last few games, it hasn't been a whole lot of fun," Bouwmeester said. "It was kind of uplifting."
Jokinen scored from the point 3:44 into OT and he was quickly mobbed by his teammates. Jokinen surely needed the emotional lift after admitting this week how much trouble he had moving on from accidentally slicing Richard Zednik's throat with his skate.
"I saw an opening," Jokinen said. "There was a free lane to shoot and I was able to hit the net and it went in."
Panthers goalie Craig Anderson made 40 saves.
"That's what you want from a backup goaltender," said Panthers coach Jacques Martin. "He hasn't played a lot, but it's nice to see him get a positive result."
The Flyers dropped to 0-8-2 in their last 10 games, matching a franchise-worst 10-game winless mark they suffered last season when they were the worst team in the NHL.
This year promised to be different and the Flyers spent most of the year contending for the top spot in the Eastern Conference. Their wretched February, however, ended any ideas about a No. 1 seed. Now, they're in a mad scramble for the eighth seed and it's not looking good.
"There was a lot of good that happened in the game, but not enough good to get you two points," said Flyers coach John Stevens.
"I thought we deserved a better fate," Holmgren said.
Briere had heard boos of late, including during pregame introduction, because he's underachieved in the first season of a $52 million, eight-year contract. Briere had lost confidence and struggled scoring 5-on-5, a slump he couldn't hide from with the Flyers in a funk.
Briere put the Flyers up 1-0 on a power-play goal with 3:40 left in the second. Briere popped out with the puck from behind the net and knocked it off Anderson's pad and through his legs for his first goal in six games.
Briere, who scored his 11th power-play goal of the season and 22nd overall, let out some pent up celebration. He pumped his fist and thrust his right arm in the air as his teammates came over and slapped him on the head.
One fan held a sign that read, "I Still [Heart] Danny."
"It's amazing right now how everything is happening," Briere said. "It's important that we keep sticking together. We can't start blaming each other. That's the dangerous part. We're going to break out of it and we're the only ones who can snap out of it."
Richards played in his 200th career game. ... The Flyers dropped to 23-1-1 when leading after two periods. ... They also fell to 23-6-9 when scoring the first goal of the game.