Controversy struck in the 66th minute when Eels five-eighth Corey Norman was sin-binned for obstructing Cowboys opposite Michael Morgan in an attempt to score off a Johnathan Thurston grubber kick.
It was an untimely exit for Norman, as his side had a slender and unlikely 16-14 lead at the time.
Johanthan Thurston levelled the game off an ensuing penalty goal, while the Eels were left to rue playing with 12 men as North Queensland ran away with a huge win in the end.
The first five minutes featured the strangest passage of play 1300SMILES has seen this season, with the Cowboys knocking on coming out of their territory two sets in a row.
There were charge-downs and hospital passes, and Parramatta were licking their chops at multiple red-zone scoring opportunities.
But the Cowboys held tough, and hit pay dirt on their first opportunity down the other end.
After a cheap penalty marched them into the Eels' danger zone, halfback wizard Thurston fired the first shot in his long-time rivalry with fellow veteran Beau Scott, releasing Gavin Coper with a neat inside ball once seeing that Scott had over-chased to leave a gaping hole on the edge of the ruck.
The hosts were in again after 20 minutes when Matt Scott punched a hole right through Parramatta's middle third, before Michael Morgan straightened his run and found Coote on a perfect supporting run for a try.
Danny Wicks looked a moral to put Parramatta's first points on the board, but was caught an inch short of the goal line. They would again fail to make use of good field position, while the Cowboys went down the other end in search of more points.
They turned down a penalty goal opportunity right in front before taking another chance right on the half-time bell to extend their advantage.
Up 14-0 coming out of the sheds it seemed like a textbook Cowboys runaway win in the making. Instead it proved anything but.
While they handled Parramatta's defensive jamming with ease in the first 40 minutes, the Cowboys were made to pay not just once but twice in the second as Semi Radradra and Michael Jennings both bagged runaway tries after forcing turnovers in the space of 12 minutes.
First Radradra did it all himself, crunching Justin O'Neill in a tackle, picking the loose ball and outsprinting the Cowboys' convoy of chasers.
Radradra scored again 10 minutes later when Norman slipped a grubber kick through, before Jennings intercepted a Thurston pass to run away for a long-range four-pointer.
Fullback Michael Gordon gave them the 16-14 lead with the conversion, but as usual the home side did not panic.
The game's hit of controversy came from Morgan being obstructed in a kick-chase by Norman, who was subsequently sent to the sin bin, as Thurston evened the score at 16 apiece with 14 minutes to play.
The lack of numbers proved too much for the Eels, who gave up a go-ahead try to Antonio Winterstein five minutes later.
From there it was a typical late-game Cowboys riot, with Morgan selling a fancy dummy to a sluggish Tepai Moeroa and slicing through the score untouched off a scrum play.
Both sides were riddled with errors as the Eels tried to engineer points while the Cowboys could not handle to pill coming out of their own territory.
Morgan put it to bed with 29 seconds remaining off a fast-break chip kick from Kyle Feldt.
The second-placed Cowboys hit the road to face Manly on Saturday night, while Parramatta is at home to the Bulldogs on Friday night.
North Queensland Cowboys 32 (Michael Morgan 2, Gavin Cooper, Lachlan Coote, Antonio Winterstein tries; Johnathan Thurston 6 goals) def. Parramatta Eels 16 (Semi Radradra 2, Michael Jennings tries; Michael Gordon 2 goals) at 1300SMILES Stadium. Half-time: Cowboys 14-0. Crowd: 19,308. Holden Cup: Cowboys 54-12. Sin bin: Corey Norman (Parramatta Eels – obstructing kick-chaser), 65th minute.