Rovers trailed thanks to Lloyd Dyer's 16th minute strike, but it was David Nugent's controversial penalty, after Tommy Spurr was adjudged to have fouled Ritchie De Laet on 45 minutes, that put the game firmly in the favour of the home side.
The Rovers boss was pleased with the way his side rallied in the second half, getting their rewards when substitute Chris Taylor was flattened in the box and Jordan Rhodes converted from the spot.
Rovers pressed for a leveller that their second half display merited but they just came up short.
"We shot ourselves in the foot with their first goal with the way we gave it away and then it is a big call right on half-time," said Bowyer.
"If we'd have gone in 1-0 down then it might have been a little bit different. It is a big call from the linesman and I just felt that the referee needed to be stronger because he's got the same view as me and the same view is that Tommy Spurr played the ball first.
"There was only one lad from the Leicester team that appealed. It was a contentious decision right at the death of the first half.
"At half-time we are 2-0 down and we said to the lads, listen if we are going to lose the game, then we have a good go fighting and we get ourselves back in it.
"On another day Tom Cairney's shot at the death might have gone in and if we'd have got a goal earlier you never know.
"At the death you hear the crowd encouraging the ref to blow for full-time because they were anxious a little bit.
"That tells you how we were doing, we were giving it a right good go."
Rovers are back in action this Saturday when Huddersfield Town are the visitors to Ewood Park.
Tickets are on open sale up until the 3pm kick-off, priced from £19 Adults, £12 Seniors and £7 Juniors. Book online today at www.onerovers.co.uk