Manly are set to miss out on the finals for the first time in over a decade after succumbing 30-12 to North Queensland at Brookvale Oval on Monday night, with a shoulder injury to Daly Cherry-Evans adding to the Sea Eagles' misery.
Antonio Winterstein scored two first half tries and Michael Morgan scored one second half try and set up another as the Cowboys held onto second place on the NRL ladder.
Cherry-Evans suffered a first half shoulder injury attempting a tackle on Gavin Cooper and didn't return after the break.
Cowboys prop Matt Scott left the field early in the second half due to a knee injury and also didn't make it back on the field.
Antonio Winterstein opened the scoring for the visitors in the seventh minute from a Johnathan Thurston kick as the Cowboys dominated the opening exchanges.
Cherry-Evans hit back against the run of play for Manly in the 17th minute when he pounced on a loose Winterstein pass that Scott couldn't handle and kicked twice for himself and scored untouched.
But from then on, off the back of a forward pack making big metres, it was all the Cowboys.
Kane Linnett scored the visitors' second converted try in the 28th minute before Thurston added another penalty goal to his tally. Winterstein then grabbed his second try of the night on the back of a 70m movement in the 38th minute for a 20-6 lead at the break.
Manly gave themselves a chance of a fightback when Brett Stewart scored his 86th try at Brookvale just three minutes after halftime before 7,643 fans.
But without Cherry-Evans the Manly attack couldn't find a way through or around the Cowboys.
Michael Morgan sliced his way through the Sea Eagles line from short range for the visitors' fourth try of the night in the 59th minute, and when Morgan helped create Jake Granville's try in the 65th minute the result was beyond doubt.
Manly last missed out on the finals in 2004, but now need to win all of their final seven to guarantee a top eight berth, a tough prospect given they face the Warriors, Brisbane and South Sydney in the next three weeks.
The Cowboys have now won 13 of their last 14 games and eight straight on the road.
Cowboys coach Paul Green said it was another important win for his side.
"Sometimes coming off a bye you can be a bit flat, but we played with some good energy," he said.
"Brookvale Oval is a hard place to win at, so that was very pleasing.
"Defence is a part of our game we need to improve and I was happy with the way we defended.
Green said Morgan had come out of his debut State of Origin series full of confidence.
"As coaches we complain about it but he has taken a lot out of it," Green said.
After two successive wins threatened to turn Manly's season around, coach Geoff Toovey wasn't happy.
"We just made too many mistakes and against quality sides you can't afford to do that," he said.
"And we had a few opportunities (to come back into the match) but weren't good enough to take them.
"It is disappointing to play like that at home. That loss at home means we have to win another on the road."
Manly officials said Cherry-Evans aggravated a left shoulder injury and he will undergo scans on Tuesday.