Patrick Marleau and Dan Boyle had two assists each and backup goalie Thomas Greiss stopped 37 shots for the Sharks, who won for the fourth time in five games to complete a 4-2 trip. The Sharks won 4-3 at Atlanta on Saturday and turned in another impressive effort against the Flyers.
"It's great to get the win as it made our road trip," Malhotra said. "We played a lot of tough teams to go 4-2, but it's nice to score, too."
Greiss thwarted the Flyers on a number of chances in front of the net, which allowed the Sharks to build on their lead.
"He stepped up," San Jose coach Todd McLellan said. "It probably wasn't fair to throw him out there to the wolves, but it shows his character. He's been practicing hard. Maybe he knew it was coming and his teammates rallied around him."
Darroll Powe scored the lone goal for the Flyers, who had their two-game winning streak snapped.
"I think we had some chances there," Philadelphia coach John Stevens said. "You start chasing and it's a tough way to win a hockey game."
Philadelphia goalie Brian Boucher stopped 24 shots in his first start of the season. Boucher, who played for the Sharks last season, started for the Flyers for the first time in more than seven years. He made his debut with Philadelphia in 1999 and has played for five NHL teams since then.
"It would have been nice to win," Boucher said. "It didn't work out that way. It was a starting point."
Flyers captain Mike Richards was in the lineup after being cleared by the NHL for a hard hit on Florida left wing David Booth in a 5-1 win over the Panthers on Saturday. Booth left the ice on a stretcher with 2:55 left in the second period following a blow to the face. He was transported to an area hospital and remained overnight for tests before being released on Sunday.
The Sharks went ahead 2-1 at 7:51 of the second period on Malhotra's first goal of the season. The puck deflected off Boucher's stick and into the net.
Malhotra struck again slightly more than 2 minutes later with his second goal. With 9:55 left, Malhotra's wrist shot from above the faceoff circle beat Boucher for a 3-1 advantage.
"They were simple plays, simple hockey," Malhotra said. "The first, we just got to the net and we were fortunate to get that bounce. On the second, we were just trying to get them to make bad decisions and just get the puck on the net."
Ortmeyer completed the scoring with a turnaround wrist shot with 3:09 left.
San Jose took a 1-0 lead when Heatley scored his eighth goal of the season, a power-play goal at 6:20 of the first period. Joe Thornton and Boyle registered assists on Heatley's goal as he capitalized on a second chance in front of Boucher.
The Flyers tied the game at 9:44 of the first. Mika Pyorala earned his first NHL point with a pass to Powe, who sent a one-timer from above the slot into the net.
Flyers C Danny Briere played in his 600th career game. ... San Jose improved to 7-0 when leading after two periods. ... The Flyers recalled defenseman Oskars Bartulis from the Adirondack Phantoms of the American Hockey League. Bartulis has two goals and one assist in eight games with the Phantoms this season. ... San Jose played without RWs Devin Setoguchi and Ryan Vesce. Both players suffered leg injuries in Saturday's 4-3 win at Atlanta and are considered day-to-day.