Tommy Spurr gave the visitors an eighth-minute lead before second-half strikes from Grant Holt and Emmerson Boyce won it for Wigan after Grant Hanley had been sent off just after half an hour for Blackburn.
"The players were magnificent, cheered on by a fantastic support," Bowyer told the club's official website.
"We leave here with our heads held high, but gutted that we didn't get anything from the game. We've done ourselves proud in terms of how we've dealt with ten men.
"The lads truly showed great courage today and the fact that so many of our fans stayed behind at the end to applaud them off speaks volumes."
After 11 games of the Championship season, Blackburn are five points off the top six in ninth.