While the Cowboys would go on to lose the contest, Bowen was taken from the field midway through the second half with a leg injury.
It's now feared by the club that it'll be a season-ending ACL injury for the 28-year-old, who has 45 NRL games to his name.
Bowen, who is a relative of former legendary fullback Matthew Bowen, left the Cowboys at the end of 2019, but returned this season on a one-year deal.
While he struggled to find a place in the Cowboys' team during the first half of the season, he has played every game since Round 9, scoring three tries in that time.
He may have had his best game of the season against the Roosters yesterday despite the Cowboys going onto lose, despite only playing 55 minutes.
All Run Metres
Cowboys' coach Todd Payten seemed to confirm the news at the post-match press conference.
"He's really upset," Cowboys coach Todd Payten said.
"He's going to be out for an extended period. I think it's the worst."