Queensland No.7 contenders Sam Walker and Clifford had a monumental battle at Magic Round in a Saturday night arm wrestle.
Walker defended well for the Roosters and came alive late in the match.
Clifford's long kicking game was sensational and his general play composed and confident to just outpoint his opposite number.
Tricolours captain and fullback James Tedesco is in the frame for a NSW recall but was below his best with uncharacteristic errors blotting his copybook.
"I'm not thinking about (Origin) now," Tedesco said.
"I was disappointed with how I played tonight personally and that's on me. I thought us as a spine had plenty of opportunities and we didn't execute."
The Cowboys had Matt Lodge and Reuben Cotter sin-binned, with the latter's a hugely contentious moment.
In the 55th minute and with the Cowboys leading 18-6, Walker grubbered close to the line and Cotter grabbed him a second before the Roosters playmaker touched the ball with his thumb.
It was ruled a professional foul in a try-scoring situation and a clearly unimpressed Cotter was marched for 10 minutes.
"I wasn't happy with the call. I thought maybe a penalty but definitely not a sin bin," Cotter said.
Walker made the most of the one-man advantage with a stellar cutout pass for makeshift winger Hugo Savala to score.
The Roosters, who made 15 errors, threw everything at their opponents but the Cowboys were defiant.
"We didn't execute well for most of the game," Roosters coach Trent Robinson said.
North Queensland were magnificent in defence and mentality without big guns Tom Dearden, Jason Taumalolo, Jeremiah Nanai and Murray Taulagi.
"That's as good a win as I've had as head coach at this club in six years," Cowboys coach Todd Payten said.
"It was really composed and gritty. We had 12 men for 20 minutes and everyone turned up, worked hard and found a way. We won it off the back of our defence."
There was a magic moment for Cody Ramsey in the 10th minute, the Roosters winger scoring his first try in 1351 days after an inspired recovery from ulcerative colitis.
The Roosters lost winger Daniel Tupou to a leg injury in the sixth minute.
His replacement, Junior Pauga, was soon off for an HIA after a dangerous tackle by Cowboys centre Tom Chester, who was put on report.
Roosters prop Lindsay Collins followed Pauga when he was hit high by Lodge.
From that moment Payten's men dug deep and scored three tries in a crucial nine-minute period. Clifford set up Burns for his first with a silky cutout pass.
Debutant five-eighth Liam Sutton then had a dream moment when he lobbed a precision bomb that Roosters centre Robert Toia dropped straight into the arms of fullback Scott Drinkwater.
Burns, who left the field with a hamstring injury in the second half, was on the end of a sweeping movement to score his second in the corner to secure an 18-6 halftime lead.
A 60m torpedo by Clifford that pulled up centimetres from the dead ball line was a highlight of the second-half early stages.
The momentum swung with the Cotter binning but the Cowboys hung tough to earn a deserved win and one of their best.
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