The Sea Eagles looked uncomfortable from the start, away from their traditional fortress of Brookvale Oval and missing the toughness and workrate provided by the suspended Glenn Stewart.
The Cowboys gained confidence as the first half wore on, with their forwards gradually gaining some ascendency, led by Matt Scott and the workaholic Aaron Payne.
This year has been a remarkable turnaround from the Cowboys, considering they have won just five matches last year and lost 11 games on the bounce.
It was a scrappy, uncertain start from both sides, with a surfeit of try-scoring opportunities. That was a surprise, especially considering they represented the most potent attacking teams (Manly 98 tries, North Queensland 97 tries) of the regular season.
Manly dominated the opening quarter, before the Cowboys, inspired by Johnathan Thurston came back into the game.
For the first time in nine matches, the Cowboys were first try scorers.
After forcing a repeat set, Willie Tonga dotted down for the visitors in the 29th minute, snaring a Thurston chip after a sumptuous piece of deception by the halfback.
Manly were a frustrated team in the first period, trailing heavily in the penalty count and not playing the kind of football of which they are capable.
The Cowboys had early chances in the second half, before William Hopoate eased some Manly and Warriors' nerves with a try in the 48th minute, after good work from Cherry-Evans.
Just under 10 minutes later, the Sea Eagles were soaring again, with Foran providing a spectacular one-handed offload for Brent Stewart to score.
With gathering momentum came luck for Manly, as a Cherry-Evans bomb deflected off a goal post and bounced into the path of Anthony Watmough, who gleefully grabbed Manly's winning ticket.
Stewart, Matt Ballin and Jamie Buhrer scored late tries to add to the Manly joy as the Cowboys seemed to clock off early - their minds perhaps already on Mad Monday.
Manly: 42 (W. Hopoate 2, B. Stewart 2, A. Watmough, J. Buhrer, M. Ballin tries; J. Lyon 6 goals, M. Robertson goal)
North Queensland: 8 (W. Tonga try, J. Thurston 2 goal).
Halftime: 0-8.