But he redeemed himself with a piece of special play that was almost impossible to defend, throwing a huge dummy before blowing through a hole to break Brisbane's heart.
The Cowboys led 16-8 at halftime.
It would have been a greater margin had winger Ashley Graham not spilled a perfect pass from teammate Ray Thompson with the Broncos' line wide open.
Brisbane came out in the second half to post two converted tries in eight minutes.
Bench forward Josh McGuire couldn't believe his luck, swooping on one of Bowen's spilled balls.
The Broncos were in again when centre Jack Reed delivered a one-handed looping pass to winger Gerard Beale for Brisbane to lead 20-16 before the enigmatic Bowen scored the first in his double off a lovely Johnathan Thurston pass.
The Cowboys were helped considerably in the first half by a 7-3 penalty count.
Their opening try of the match, however, came from some poor Brisbane defence with lock Dallas Johnson ambling across in just the fifth minute without being touched.
Brisbane replied when winger Jharal Yow Yeh slid over in the right corner following a quick shift and spread with skipper Sam Thaiday, playing his 150th game for the club, delivering the last pass.
Bowen arrived too late to stop the try and his knees came into contact with Yow Yeh, who for a few seconds appeared injured.
The result ended Brisbane's nine-game winning streak at Suncorp Stadium and reassured Cowboys' fans that the 18-0 loss to the Gold Coast the previous weekend was an aberration.
NORTH QUEENSLAND 28 (M Bowen 2 D Johnson J Segeyaro B Tate tries J Thurston 4 goals) bt BRISBANE 26 (G Beale J McGuire B Te'o J Yow Yeh tries C Parker 5 goals) at Suncorp Stadium. Referee: Jason Robinson, Gavin Reynolds. Crowd: 43,171.
- AAP
