The result moved the Hurricanes, who had a 4-0 lead early in the second period, a point ahead of the Senators in the Eastern Conference standings.
Carolina is 11-0-1 in its last 12 home games against Ottawa.
Eric Staal, Riley Nash and Tuomo Ruutu also scored goals for Carolina, which won the first meeting of the season 4-1 on Nov. 24 in Raleigh. Andrej Sekera, Alexander Semin and Drayson Bowman had two assists apiece for Carolina.
''We made a few mistakes and kind of blamed it on a few brain cramps with the afternoon game,'' Hurricanes coach Kirk Muller said. ''But we came back in the third, just calmed down and started all over again. We said 'Hey guys, we're playing well, but we just made a few mistakes with turnovers.' I thought we had a good, solid third period.''
Kyle Turris scored his 16th and 17th goals of the season for Ottawa, which also got a goal from Mike Zibanejad. Clarke MacArthur and Eric Gryba each had two assists for Ottawa.
Carolina goalie Anton Khudobin had 23 saves.
Ottawa goalie Robin Lehner, playing for the first time in five games, was pulled after the second period with the 5-3 deficit and finished with 17 saves. Craig Anderson stopped nine in the third.
The most recent Ottawa win at Carolina was a 3-2 shootout on Oct. 25, 2011.
''You can't play catch-up hockey all the time and expect to have any chance of being successful consistently,'' Ottawa coach Paul MacLean said. ''Today we played catch-up the whole game. We turned over pucks, we didn't put it in the right spots and we didn't compete hard enough in the defensive zone.''
The game was originally scheduled for Friday night, but was postponed because of the NHL rule prohibiting teams playing three days in a row.
The Hurricanes' game at Philadelphia on Tuesday night was postponed to Wednesday because of the winter storm and the team was at Buffalo on Thursday night.
Gerbe got Carolina's first goal at even strength at 10:30 of the first.
Carolina then outshot the visitors 16-9 in a wild second period that produced seven goals.
Staal put the Hurricanes up 2-0 on a breakaway at 6:05 of the second for his 12th of the season.
It went to 3-0 just 22 seconds later on another rush, as Malhotra took Gerbe's pass from the left boards on the glove-side doorstep and buried the puck. Nash made it 4-0 at 13:23.
''When we put that individual game focus into things, the games are going to take care of themselves,'' Malhotra said. ''Once there's a break we can see where we are in the standings. But as far as the games are concerned we have to keep our individual game focus and get our points when we can.''
Turris broke the shutout at 13:58 with his 16th goal of the season, and then added a short-handed goal at 17:45.
Ruutu fired in an unassisted power-play goal from the high slot at 19:27 to make it 5-2.
But Zibanejad scored 10 seconds later to finish the period's scoring.
''The second period was good for a while and then it got interesting,'' Hurricanes captain Staal said. ''They've got some skill and some talent, and if you get a little bit loose they can make you pay.
''But I thought we really regrouped well in the second intermission and really closed it out in the third, didn't give a lot.''
Malhotra added an empty-net goal at 18:19 of the third.
NOTES: The teams will play again this season on March 31 in Ottawa. . Carolina D Mike Komisarek has a two-game assist streak for the first time since Oct. 29, 2011. . Hurricanes D Patrick Dwyer was out for his second straight game (upper body). . Ottawa RW Mark Stone (upper body) missed his third straight. . Former Carolina D Joe Corvo was a healthy scratch for the Senators. . Carolina completes its two-game homestand on Monday against Columbus. . Ottawa ends its four-game road swing on Tuesday night at Columbus.
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