Michalek scored his 17th goal 11:26 into the second, and Marleau got his 34th goal at 12:44 as the Sharks made the most of consecutive power plays after Ottawa defenseman Brian Lee had an unsportsmanlike conduct penalty added to his holding minor.
"On the bench we felt the momentum was kind of changed when that happened and then we really wanted to bear down and make them pay," said San Jose center Joe Thornton, who got his 54th assist on Marleau's goal. "We did that and that was the reason we won."
Brian Boucher made 23 saves for the NHL-leading Sharks, who ended a four-game winning streak one night earlier with a 4-1 loss in Detroit.
"Special teams are huge," Boucher said. "If you can win the special-teams game, you're going to win a lot of hockey games and it seems like we've done that this year. It was probably not a good play by Lee -- I'm sure they're not happy about it -- but good for us to capitalize on it."
Mike Fisher scored a power-play goal in the first for Ottawa, which has lost four of five (1-3-1) following a season-high five-game winning streak.
"For the most part we played pretty well," Fisher said. "We created some chances and even late, we had some point-blank chances and Boucher played really well. It was just in the second period, with some discipline. Everyone knows that they have a great power play and that was the game."
Lee had finished serving a hooking minor moments earlier when he was sent off again for holding Mike Grier at 9:39. The rookie defenseman put his team in an even deeper hole when an unsportsmanlike conduct minor was tacked on.
"I feel responsible for the loss," said Lee, who acknowledged that he had argued the holding call.
"It was a tough one, to get a double like that, but emotions are flying and it's part of the game," Fisher said. "We've just got to make sure we learn from it."
Michalek jammed the puck past Auld to draw San Jose even with 13 seconds remaining in Lee's first minor.
Marleau put the Sharks ahead moments later when Jeremy Roenick drove a one-timer from the slot that went off the San Jose captain's skate and into an open left side.
The goal was originally credited to Roenick, who has only three goals this season and hasn't scored since Dec. 6.
"He's already got 500 goals so I don't think he really cares," Thornton said. "Patty's got a good shot at it but J.R.'s past 500 so there's no big deal for him, I don't think."
Fisher opened the scoring with his ninth goal 13:46 in. The center deflected defenseman Chris Campoli's shot past Boucher while San Jose left wing Tomas Plihal was serving a tripping penalty.
"I saw the shot but it was a good tip by Fisher," Boucher said. "It was going more blocker side, he tipped it and it went glove side, so that's how you score goals nowadays. You've got to get in front of the net and you've got to have some courage to stand there and tip pucks."
Sharks RW Claude Lemieux was a healthy scratch for the first time in his return to the NHL. The 43-year-old Lemieux has one assist in 15 games since he was called up from Worcester of the AHL on Jan. 19. "I feel great, but it probably won't hurt me to get the night off," Lemieux said. ... LW Christoph Schubert and Ds Brendan Bell and Alexandre Picard sat out for Ottawa.
Copyright by STATS LLC and The Associated Press
Arena: Canadian Tire Centre Location: Ottawa, Ontario
Referees: Greg Kimmerly, Paul Devorski Linesmen: Tim Nowak, Anthony Sericolo
Attendance: 17,791 (96.2% full)
Team Stat Comparison
Power Play Goals
Power Play Opportunities
Shots on Goal
Mike Fisher (9)
(Power Play) Assists: Chris Campoli, Dany Heatley
Milan Michalek (17)
(Power Play) Assists: Joe Pavelski, Marc-Edouard Vlasic
Patrick Marleau (34)
(Power Play) Assists: Jeremy Roenick, Joe Thornton