Whilst results elsewhere ensured Rovers' outside chances of a top six finish ended, they finished the season a very creditable 8th place with 70 points.
Added to that Rovers ended the campaign 12 matches unbeaten, the victory over Wigan Athletic ensuring they finished with a hat-trick of victories.
"Our objective at the start of the day was to win the game and that is what we've done," Bowyer told Radio Rovers.
"Full credit to the lads, I thought our football at times going forward was outstanding, Carson has had to make some saves and we had further opportunities as well, we rattled the bar and had a goal disallowed.
"I'm delighted that we've kept the 12-game unbeaten run to end the of the season."
Rovers were a threat throughout, with attacking play that left the manager drooling.
"You've seen what a threat that we've got going forward, Kingy's pace frightened them, Rudy, what can you say about the big man, what a contribution he's made to the football club.
"Jordan Rhodes gets his 25th, he's scored more than 100 goals in four years, which is phenomenal and the creativity of Cairney, what a goal that was. If it was in the Premier League or abroad there would be reruns of it all night.
"I've nothing but praise for them, they keep going, they've a great spirit, they can have a good summer because they've started the rebuilding process."
The manager reserved his last word for the fantastic support his side has received all season, delighted to send them all home happy.
"A huge thanks to the fans," added Bowyer. "We need everybody to get to where we want.
"They've been phenomenal for me and the players this season."