The captain put his team equal on 15 minutes with a trademark dash from dummy half and passed inside for second rower Liam Fulton on 21 minutes to bash over and take advantage of some slack Cowboys tryline defence.
That defence again cost the Cowboys, Fulton finding himself in plenty of space and offloaded for injury replacement Masada Iosefa to score underneath the posts on 31 minutes.
But despite the Tigers' dominance, the Cowboys managed to stay in touch with two good team tries inspired by Bowen.
Bowen was integral to a stunning team try on 24 minutes, receiving the ball on his own 30 metre line and running at the line before setting up Faifai Loa to score in the corner.
Down 16-10, the Cowboys fullback collected a ball from a turnover in the 36th minute and put centre Brent Tate through to score to make it 16-16 at the break.
While the Tigers dominated the first half it was mostly the Cowboys in the second and they took the lead on 46 minutes through Anthony Mitchell.
The interchange hooker was unguarded from dummy half and beat three defenders to grab his first try since moving to Townsville.
Bowen put the match beyond reach in the 77th minute, his drop-goal attempt taking a fortunate deflection to give the Cowboys a seven-point advantage.
Gavin Cooper rubbed salt into the wounds on 79 minutes when he pounced on a Johnathan Thurston grubber to score.
The Tigers' injury toll also included losing five-eighth Curtis Sironen to an arm injury in the first half and Iosefa to a knee injury in the final 10 minutes.
Tigers coach Tim Sheens said the injury toll had been too much in the end, with Chris Lawrence (suspected high ankle sprain), Sironen (shoulder) and Matt Groat (under-20s, broken thumb) all taken to hospital for treatment.
"We're still disappointed in losing the game considering some of the options we took but, given we were struggling with numbers, I guess there's some solace.
"And the fact we attempted 200 tackles in the second half and only had 14 misses was a pretty good effort," Sheens said.
"It's just one of those days, some days it happens that way but the effort was great."
Cowboys coach Neil Henry praised his side's improved defence in the second half, but said there was still a lot of work to be done to overcome the slow start.
"We conceded three tries and I thought they went through our line pretty easily and we needed to fix up our marker defence and needed a bit more discipline around the ruck and to the boys credit we did, there were no points in the second half," Henry said.
"We controlled our possession much better and our men in the middle went forward well."
Cowboys co-captain Matt Scott praised Bowen's effort.
"He's defied a lot of critics I think," Scott said.
"His knees seem to be pretty much sorted and it makes such a difference to start our sets out with momentum he's gaining.
"He's making a lot of metres at the moment at the back and in broken play he's such a wonderful player."
- AAP
