Both teams were stoic in defence in the tight contest, where a Jamie Lyon penalty proved to be the difference.
The Sea Eagles now jump over the Cowboys and Brisbane into fourth spot, but will need to wait until the Broncos play Canberra in the national capital on Sunday to see if they can stay there.
The Sydney team started strongest and looked to have grabbed the first try of the night in the 11th minute when Tony Williams pounced on a Kieran Foran grubber.
But the video referee judged Anthony Watmough had impeded Cowboys defender Glenn Hall.
After an extended period of possession, the defending champions eventually opened the scoring on 25 minutes, Foran skipping past a slipping Dallas Johnson from the scrum base.
The try seemed to spark some life into the Cowboys attack and they had two scoring opportunities in as many minutes from the boot and stunning run by fullback Matt Bowen.
Starting off the second half as they finished the first, the Cowboys came out strongest in the second half.
Kane Linnett took advantage of a miscommunication between David Williams and Daly Cherry-Evans, the Manly pair not making any attempt to catch a Bowen bomb in the 52nd minute.
The ball bounced off Cherry-Evans' leg and Linnett beat the two Manly players to put the Cowboys on an even pegging.
Manly looked to have taken the lead again through Brett Stewart, after the fullback fought his way across the line in the 63rd minute, but the video referee again intervened saying centre Steve Matai had impeded Brent Tate.
But the Sea Eagles did take the lead four minutes later, Cowboys back-rower Gavin Cooper penalised for being offside in front of the posts and Lyon opted to kick the two points.
The Cowboys had a chance to score at the death, but were penalised for being offside while trying desperately to get across the tryline.
Manly will have to see whether the match review committee charges Darcy Lussick with a high elbow on Ashton Sims in the 45th minute, while Matai went off the field injured in the 67th minute with an ankle injury.
The Cowboys have their own injury concerns, with starting halfback Michael Morgan leaving the field with a shoulder injury in the 71st minute.
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