The Cowboys had four players backing up from the midweek blockbuster in Sydney, although Murray Taulagi (shoulder) and Reece Robson (neck) sat out Saturday night's match.
Fresh off the bye, the Warriors had six players bringing a swag of experience back on deck, including prop Addin Fonua-Blake, hooker Wayde Egan and fullback Charnze Nicoll-Klokstad.
The two teams' first-half energy levels couldn't have been more contrasting, with the Warriors scoring four tries to lead 22-0 before North Queensland got on the scoreboard.
Cowboys coach Todd Payten said he had no regrets about allowing his Origin contingent to back up, but felt their teammates needed to lift.
"It's a tough ask, I've got no doubt, but they pride themselves on backing up," Payten said.
"The guys around them have to provide the energy and spark, not them, and that's what we've got to understand and get better at if we do it again.
"Our energy was down ... we started poorly, dropped the first set, gave away a penalty in the second set and were just beaten at the ruck.
"We gave them too many opportunities in our own end - it was 40-odd plays inside our 20 and we made 80 or 90 more tackles, so it was disappointing."
Nicoll-Klokstad showed individual brilliance to beat three defenders and conjure the opening try in the eighth minute.
Fonua-Blake, who was stood down for the New Zealand side's last-up win over the Dolphins after he skipped the team song following the round-11 victory over Penrith, crossed in the 13th minute to lead the team's tryscorers for the season.
While an error by Queensland Origin five-eighth Tom Dearden contributed to Fonua-Blake's four-pointer, the Cowboys playmaker also set up his side's only try of the first half.
He scooted out of dummy-half deep in his own end and raced 30 metres before offloading to fullback Scott Drinkwater, who ran the distance to touch down shortly before halftime.
Dallin Watene-Zelezniak extended the visitors' margin after the break with their fifth try, and the Warriors winger was then involved in a miracle effort in the 68th minute.
On the last tackle, Nicoll-Klokstad put a kick into the in-goal and somehow Watene-Zelezniak was able to bat the ball back as he dived over the dead-ball line - it fell into the arms of his fullback, leaving Cowboys defenders stunned.
Braidon Burns offered a late response for the Cowboys' second try of the night but the Warriors had the final say with Rocco Berry, in his return from a hand injury, bagging his second of the night as the clock ticked down.
The win was the Warriors' third in row, continuing their mid-season resurgence.
They also have star halfback Shaun Johnson and centre Roger Tuivasa-Sheck to return.
Both teams had players sent to the sin bin in the second half, but neither Chad Townsend nor Chanel Harris-Tavita are expected to face any further penalty following their minor altercation.
Warriors coach Andrew Webster said his team entered the match bristling with belief.
"That's what we've been working towards, we won two in a row before the bye and came in with plenty of confidence," Webster said.
"We knew if we did what we wanted to do we would get what we wanted, and the boys were great."
