A first-half strike from Mauro Boselli was enough to settle a closely-fought tie in Wigan's favour, although the Premier League side had the woodwork to thank for preventing an upset as Eunan O'Kane and Marc Pugh rattled the crossbar during the 90 minutes.
It is the first time Howe has tasted defeat since he returned as Cherries boss, a run of 18 matches, but the former Burnley boss was pleased with the effort from his side.
"I thought it was a really good game and Wigan showed us a lot of respect with the team they picked," he said. "It was a strong team and we were slightly disappointed with our first-half performance.
"I think in the second half that all changed and we had a right go at Wigan and threw everything at them and, apart from their goalkeeper making some good saves and the woodwork, I think we would have deservedly forced extra-time.
"I think it was a really good effort from the players, we did not necessarily lose it and I think Wigan won it - if a team was going to beat us they were going to have to earn it."
Wigan counterpart Roberto Martinez was also impressed by what he saw from a battling Bournemouth outfit.
"It was a very difficult game as we expected," he said. "We know Bournemouth have been unbeaten and it doesn't matter at what level you do that at because you have got a very strong unit.
"I must admit Bournemouth deserve huge, huge credit over the two games in the manner they play football and I think it is going to bring real success to this football club."