Down 32-6 at one stage, the Tigers scored three tries within five minutes in the second half and got to within four points when fullback Jahream Bula crossed with five minutes left on the clock.
Adam Doueihi missed a tough conversion, which would have allowed them to level with a two-point field goal.
It left the visitors unable to complete one of the NRL's greatest fightbacks, just falling short at Queensland Country Bank Stadium in their Saturday night clash.
The Tigers were left to rue ill-discipline in the first half.
Turning out for their first match since the departure of polarising playmaker Lachlan Galvin to Canterbury, they did themselves no favours with both Jarome Luai and Adam Doueihi sin-binned.
Luai had a stint on the sidelines from the 11th minute for slowing down the ruck after repeated team infringements as the Cowboys attacked the line.
While the star halfback was off the field, John Bateman, who had an acrimonious split with Wests Tigers, scored the opening try for North Queensland.
Centre Jaxon Purdue also crossed in the 16th minute while the visitors were down a man.
The Cowboys then took advantage of centre Doueihi making a temporary exit for a professional foul, with Scott Drinkwater crossing for an 18-6 halftime lead.
That margin proved a mountain for the visitors, made larger just two minutes into the second stanza with Doueihi still off.
Skilful second-rower Jeremiah Nanai, backing up from State of Origin duty, leapt high to take a kick and than raced to the line to score his team's fourth try.
While the Tigers looked out on their feet in the second half, the Cowboys' other Queensland Origin stars Tom Dearden and Reuben Cotter also stood up.
Dearden added a 57th-minute try to his two try assists for a 32-6 scoreline.
The tide then turned for the Tigers in the 62nd minute when centre Starford To'a crossed for his second, after a first-half try.
That was quickly backed up by five-eighth Heath Mason, and then Charlie Staines three minutes later, for a 32-24 scoreline to put the Cowboys crowd on edge.
Bula had them on their feet with his late four-pointer but the home side managed to hang on for the win.
North Queensland will move to sixth place on the competition ladder on the back of their first win since round eight.
It's a third straight loss for the Tigers, who sit 13th.
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