Lee Chung-Yong opened the scoring for Bolton before Lukas Jutkiewicz's magnificent strike from long range in the 32nd minute saw them double their lead in the Sky Bet Championship tussle.
Howe said: "I felt we deserved to win. I was disappointed that we didn't take all three points.
"It's mixed emotions for me because when you're two-nil down you're delighted to come back and get anything. But for the majority of the game I think we passed the ball better than Bolton, dominated possession and had more chances so it was a strange game.
"We felt that if we could get the first goal we'd have a really good chance of winning the game. Thankfully from going two goals down we responded really well."
Howe also suggested his team have grown as the season has gone on.
He said: "We took a couple of heavy beatings early on in the season and didn't respond well to chasing games.
"I think that we've learnt from that. I think we are a better side now and we showed good maturity here not to panic and try and chase the game early.
"We made good decisions with the ball and once we believed in how good we can be, then I think you saw a really good Bournemouth performance."