Bergenheim was playing in his 10th game after dealing with lower-abdomen issues since the 2012 Stanley Cup Playoffs. His prior goal came April 24, 2012 in Game 6 of the Panthers' Eastern Conference Quarterfinal series against the New Jersey Devils.
"I still have stuff to work on," Bergenheim said. "I feel all in all that it's coming after the surgeries. It's coming. It's not there yet, but it's getting better."
Bergenheim's third career two-goal game came when he was feeling less than 100 percent, battling flu symptoms.
"Bergy has been sick still and he's playing sick," Panthers interim coach Peter Horachek said. "I told him after the game that we're going to make sure that he's sick every game if he's going to keep playing like that.
"Sometimes when you feel things and you feel the injury, it's like a knee, it's like a shoulder, you know it's there and you just kind of have to go out and play sometimes to kind of get over that and just play through it. Maybe because he wasn't feeling so good, he just forgot about it and just went out and played. He did a great job."
Bergenheim came close to his second career hat trick in the final minute but his shot toward an empty net was blocked by a Flyers player.
Thomas came into the game with a 17-4-2 record and 2.16 GAA in his career against Philadelphia, including the postseason. In his first start against the Flyers this season, Oct. 8, Thomas allowed two goals on five shots before leaving with a groin injury. The Flyers won that game, 2-1.
"I wasn't thinking of paybacks," Thomas said. "I was just thinking that we had a pretty good road trip and we wanted to start off the homestand the correct way. We need to take advantage of being at home and we did that tonight."
The Panthers, coming off a 2-2-1 road trip, began a five-game homestand that continues Wednesday against the New York Rangers and includes games against the Pittsburgh Penguins, Ottawa Senators and Winnipeg Jets.
Florida defenseman Erik Gudbranson scored his first goal of the season with 4:08 left in the third period. It was the third of Gudbranson's three-year NHL career and his first since Dec. 27, 2011, snapping a 100-game drought.
The insurance goal came when his slap shot from the point bounced off Flyers goalie Steve Mason and over his shoulder before rolling into the net.
"It's nice to get the monkey off my back," Gudbranson said. "I got a lucky bounce for it going up like that, but still it counts. I think at the end of the day our team just played a really solid game. We battled the whole 60 minutes. That's the thing to take away from that."
The win evened the Panthers' record under Horachek at 4-4-1.
Wayne Simmonds scored for the Flyers, who lost in regulation for the first time in eight games. During their 6-0-1 run, the Flyers scored 27 goals.
"We got distracted; maybe we thought we were the better team and coming here would be an easy game," forward Scott Hartnell said. "When you underestimate your opponent in this League, you're going to … lose the game. We did just that."
Flyers coach Craig Berube, whose first game after he replaced fired Peter Laviolette was the 2-1 victory against the Panthers, said he hoped his team hadn't overlooked Florida.
"Who are we to overlook anybody?" Berube said. "We talked about it before the game about being ready. I'm not sure we were."
Mason stopped 28 shots. He was 5-0-0 with a 1.17 GAA and .960 save percentage against Florida.
The third and final game between the Flyers and Panthers will be April 8 at BB&T Center.
Defenseman Mike Weaver returned to the Florida lineup after missing four games because of an illness, and he made a big impact blocking shots and helping the Panthers kill off a 5-on-3 power play for 1:23 early in the second period with the game scoreless.
"It was huge," Flyers captain Claude Giroux said. "We had our chances. Thomas comes out pretty far there. Five-on-three has to be automatic."
Twenty-nine seconds after the end of Florida's second penalty, Bergenheim opened the scoring at 3:35 of the second after a persistent effort around the Philadelphia net.
Bergenheim first tried a wrap-around with his forehand, then a wrist shot from the side of the net, and finally a wrap-around to his backhand, with the puck sliding in between Mason and the post.
"At some point it's got to go in, right?" Bergenheim said. "I think we had a good group effort there with the line. We had the guys going to the net. I had the puck and they made the room for me. That felt good."
Panthers defenseman Dylan Olsen and forward Jimmy Hayes, the players acquired in the trade that sent forward Kris Versteeg to the Chicago Blackhawks on Nov. 14, had the assists. Olsen was playing his first game for Florida after being recalled from San Antonio of the American Hockey League on Sunday.
Bergenheim made it 2-0 at 13:59 of the second when he scored on the second of back-to-back power plays. He was standing in front of the net when he tipped Marcel Goc's wrist shot from inside the top of the left circle.
Florida came in with the worst power-play percentage in the NHL (9.3) and had gone 0-for-9 in its previous two games.
Simmonds cut into the Florida lead with a power-play goal at 7:06 of the third period when he put home a rebound after Thomas stopped Scott Hartnell's one-timer from the slot.
"There's a lot of skill and a lot of veteran leadership on that team," Gudbranson said. "We knew that in the third they were going to come really hard, but we didn't break. We bent a little bit in the first and second, but for us to battle like that and pull that one off at home after that road trip is huge."
|Sean Bergenheim (1) ASST: Jimmy Hayes (1), Dylan Olsen (1)|
1 - 0 FLA
|PPG - Sean Bergenheim (2) ASST: Marcel Goc (3), Erik Gudbranson (3)|
2 - 0 FLA
|PPG - Wayne Simmonds (5) ASST: Scott Hartnell (3), Claude Giroux (13)|
2 - 1 FLA
|Erik Gudbranson (1) ASST: Scottie Upshall (8), Brad Boyes (4)|
3 - 1 FLA
|Power Play %||23.4%||16.3%|
|% on Road||18.6%||15.9%|
|% at Home||28.0%||16.5%|
|Krys Barch Instigator against Jay Rosehill|
|Krys Barch Fighting (maj) against Jay Rosehill|
|Krys Barch Misconduct (10 min)|
|Jay Rosehill Fighting (maj) against Krys Barch|
|Scott Gomez Tripping against Claude Giroux|
|Erik Gudbranson Delaying Game-Puck over glass|
|Claude Giroux Unsportsmanlike conduct|
|Braydon Coburn Cross checking against Scottie Upshall|
|Dmitry Kulikov Roughing against Claude Giroux|