After sharing a shutout with rookie Nolan Schaefer last month, Nabokov got his first since March 31, 2004, when he set a franchise record with his ninth of the season.
"It feels great, but it feels even better that we got the win, we got the two points we need and we're ready to move up," Nabokov said.
Marleau beat Dominik Hasek on a breakaway in the second and Ekman finished off a two-on-one with Joe Thornton in the third, just moments after Nabokov gloved a rolling puck just in front of the goal line to keep San Jose ahead.
"That's how it usually works in hockey, they almost score and we come back and bury that second goal," Thornton said. "It was kind of a backbreaker for them, so it was a big goal for us."
The Sharks won a season-high six straight from Dec. 2-16 and had another five-game winning streak from Oct. 26 to Nov. 4.
"You look up and see 40 shots against, but I don't really remember too many of them being grade-A chances," San Jose coach Ron Wilson said. "The shots were from the outside, the defense did a great job and our forwards competed like heck."
Ottawa lost for just the fourth time in 21 games at the Corel Centre, which will be renamed Scotiabank Place on Friday.
"I think our guys did a pretty good job of boxing them out," Nabokov said. "It was a 60-minute effort from everybody and that's what we need, and hopefully in the second half of the season we're going to have this every game."
The Senators, who beat Phoenix 6-2 on Tuesday, have lost four of their last six games, their worst stretch of the season.
"Our problem is that if we don't score five or six goals, we lose the game," Hasek said. "We have to find a way to win these games. I think they worked a little bit harder than we did. It's very important to find a way to win the close games. In the playoffs, that's what it's going to be."
Ottawa center Bryan Smolinski acknowledged that the 40-year-old goalie's comments were on the mark.
"We didn't get the second and third chances that we usually get, which is uncommon," Smolinski said. "It happens, but he is right, we do have to learn how to play those 1-0, 2-1 games. It'll come. We're halfway through the season and we've got a lot of learning to do, but eventually we're going to win."
Hasek, who made 34 saves, came up huge in the first period to keep the game scoreless. He made a desperate glove save on Ekman, who jumped on a rebound of Marleau's shot during a long five-on-three Sharks power play.
The Czech superstar also benefited from a shot off the post moments later, as did Nabokov on Ottawa captain Daniel Alfredsson's shot late in the first.
Alfredsson, who had two goals and two assists Tuesday in his return from a rib injury, saw his crossing pass in the Sharks' zone intercepted by Marleau.
"He did it before on the same shift so I was just lucky to read it and I don't think he got everything he wanted to on it and I was able to intercept it," Marleau said.
The San Jose captain raced the length of the ice and beat out Alfredsson's attempt to track him down before putting a backhand past Hasek 8:17 into the second.
Ottawa came close to tying it 1:16 into the third but Nabokov reached out just in time to prevent a rolling puck from crossing the line.
The Sharks made it a two-goal lead shortly afterwards when Thornton came in on a two-on-one and passed to Ekman, who redirected the puck past Hasek at 2:45.
"They played very good defense, but we gave them two goals and that was the game," Senators coach Bryan Murray said. "When you turn the puck over against a team with speed, that's what happens."
Nabokov injured his groin during a 5-0 win in Buffalo on Dec. 2 and was replaced by Schaefer -- who is currently playing for AHL Cleveland -- midway through the third period. Schaefer, the younger brother of Senators forward Peter Schaefer, has the Sharks' other shutout this season. ... The crowd of 19,538 was the Senators' 17th sellout of the season. ... Ottawa center Jason Spezza
missed his 10th game in the past 11 because of a chest injury. ... Senators right winger Brandon Bochenski returned after missing 11 games with a separated shoulder.
Copyright by STATS LLC and The Associated Press
Arena: Canadian Tire Centre Location: Ottawa, Ontario
Referees: Stephane Auger, Greg Kimmerly Linesmen: Michel Cormier, Derek Nansen
Attendance: 19,538 (105.6% full)
Team Stat Comparison
Power Play Goals
Power Play Opportunities
Shots on Goal
No scoring this period
Patrick Marleau (18)
Nils Ekman (9)
Assists: Joe Thornton, Jonathan Cheechoo