Playing most of the game with five defensemen, and then the latter parts of the game with four, the Sharks allowed 18 shots on goal and defeated the Flyers 3-2 in a shootout.
Brent Burns, one of four remaining defensemen, scored the game-deciding goal in the fifth round of the tiebreaker. He carried the puck down the middle of the ice, deked the puck from his forehand to his backhand and flipped it over the glove of Flyers goalie Steve Mason.
Melker Karlsson also scored in the shootout for the Sharks, who improved to 4-5 in the tiebreaker. Matt Irwin and Joe Pavelski scored in regulation for the Sharks, and goaltender Alex Stalock made 16 saves. The 18 shots were the third fewest the Sharks have allowed in a game this season.
The Sharks (37-30-8) won their second straight and moved within six points of the Los Angeles Kings for third place in the Pacific Division with seven games remaining, starting with a game Sunday at the Pittsburgh Penguins (7:30 p.m. ET; NBCSN, ROOT).
San Jose won't have defenseman Marc-Edouard Vlasic against Pittsburgh. Vlasic left Saturday with 4:15 left in the first period because of a lower-body injury. Sharks coach Todd McLellan said Vlasic would be re-evaluated when they return to San Jose after the game Sunday.
San Jose also played the final 7:23 of the third period and all of overtime without Scott Hannan, who was cut under his eye when he was hit into the boards by the Flyers' Nick Cousins. McLellan said Hannan was questionable for Sunday.
It's the second straight game the Sharks have lost a defenseman during a game; rookie Mirco Mueller sustained an injury to his left hand Thursday against the Detroit Red Wings. He already had been ruled out of the weekend games on Friday.
"When you get to four, it's pretty easy," McLellan said. "You just keep saying next. At five, which happened fairly early in the game, I thought our [defense] did a really god job and our [forwards] protected them. We played enough in the offensive zone to not have them be too taxed in our end. Where we ran into trouble a little bit was on the penalty kill against a very good power play. We managed the game well once they got hurt."
The remaining defensemen weren't complaining. Burns led the way with 27:33 of ice time, with Justin Braun playing 27:09, Brendan Dillon 23:57, and Irwin 22:11.
"I think it was an opportunity for other guys to step up," Dillon said. "Then in the third period we get down to four for most of it. Anytime you're playing more minutes, you get more comfortable and you simplify things."
The Flyers also were playing shorthanded on defense. With Mark Streit and Carlo Colaiacovo missing the game because of the flu, defensemen Mark Alt and Oliver Lauridsen were recalled from Lehigh Valley of the American Hockey League. Alt was minus-1 in 9:25 in his first NHL game, and Lauridsen was minus-1 in 10:26 in his first NHL game since the 2012-13 season. After the game, Alt, Lauridsen and forward Jason Akeson, who also was called up Saturday morning, were returned to the AHL.
"I thought we battled and guys did a good job that were just called up," Flyers coach Craig Berube said. "It's not easy for them. [We] gave ourselves a chance to win."
Jakub Voracek had two assists and scored Philadelphia's only goal in the shootout. The Flyers dropped to 3-10 in the tiebreaker this season.
Voracek has 76 points, two behind League-leader Sidney Crosby of the Penguins.
The point Philadelphia received for reaching overtime, combined with the Boston Bruins' defeat of the New York Rangers, leaves the Flyers 10 points out of the second wild card into the Stanley Cup Playoffs from the Eastern Conference with six games remaining.
The Flyers trailed 2-1 after two periods but Giroux's power-play goal at 8:37 of the third tied the game.
The Sharks had chances to win the game later in the third and in overtime, including a power play when the Flyers' Brayden Schenn was called for boarding for a hit on Irwin.
Despite outshooting the Flyers 44-18 and out-attempting them 83-47, the Sharks said they never got frustrated.
"You can't [get frustrated], really," Burns said. "You just have to keep playing."
Pavelski gave the Sharks a 2-1 lead at 16:43 of the first period on a goal that he banked off Manning's skate and under Mason. Referees had blown the play dead but video review determined that the puck crossed the goal line as the culmination of a continuous play that was unaffected by the whistle, and the goal was allowed to stand.
"Once it goes to (the NHL Situation Room) in Toronto, we're done," McLellan said. "We just stand there and wait for the call and we have to respect what the decision is."
The Sharks and Flyers each scored a goal early in the first period.
Irwin opened the scoring at 4:38 when he intercepted a clearing attempt by Voracek and scored on a shot from above the right circle. Then at 6:44 the Flyers responded with Raffl's 20th goal. A shot from the point by Nicklas Grossmann hit off two Sharks and bounced to Stalock, who knocked it off the post and to Raffl, who was in front to knock it in.
Follow Adam Kimelman on Twitter: @NHLAdamK