It was a first half in which the visitors scored with almost all of their chances as Lee Novak netted a double with Chris Burke following up for a well-taken third
Despite the mountain, Rovers did their best to climb it, Jordan Rhodes netting twice to set up a storming second half, but despite dominating the game they ultimately came up short.
"First and foremost I'm very proud of our lads and our supporters," Bowyer told Radio Rovers after the game. "In the second half they really got behind us.
"We've lost today and we've been clapped off the pitch, we drew the other day and we got booed.
"Forget the scoreline in that sense, we were outstanding, we were the better team by far."
Rovers started the game brightly but a first chance to Lee Novak was gobbled up before the former Huddersfield man grabbed a second from distance. The torrid first half ended with Chris Burke netting a third.
"We've given them three poor, poor goals, the second one is from 36 yards, it is very disappointing," added Bowyer.
"But I've nothing but pride for how we went about it, the fight and the sprit that they've shown really came to the fore today.
"At half time we said lets get the first goal, do the right things and cut out the silly mistakes and full credit to our lads they really went about it.
"We had the momentum, it was with us the whole game, not just the second half, in terms of how we played.
"It is a tough one to take because I don't think Birmingham have beat us, I think we have beat ourselves."
Rovers are back in action on New Years Day when they take on Leeds United at Elland Road.
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