Wigan dominated the game in terms of possession and chances, and could easily have doubled the winning margin such was their superiority.
Marc-Antoine grabbed the opening goal after just five minutes, with an own goal from Elliott Ward and a wonder goal from Jordi Gomez completing the scoring after the break.
"We weren't at our best today, I think that was pretty clear," acknowledged Howe.
"We didn't start the game very well - the real Bournemouth didn't turn up to play.
"We were under pressure, we gave the ball away in dangerous areas which is unlike us, and it was only in the last half hour when we came alive.
"The substitutes breathed new life into us and we showed we are a good side.
"But it's a feeling of disappointment we will leave with, because we haven't given a very good account of ourselves."
Wigan were at it right from the off, and Howe was at a loss to explain why the Cherries took so long to get into the game.
"I'm not sure why we started so slowly," he added.
"We knew what to expect, that Wigan play a high, pressing game, and we prepared for that.
"But we didn't adapt very well to the demands placed upon us and we were on the back foot right from the off.
"We'll regroup now and hopefully produce a better performance against Burton in the FA Cup on Tuesday night.
"You have to learn from every defeat, and it's important we use experiences like this to move forward."
First-team coach Graham Barrow faced the media for Wigan, with Uwe Rosler otherwise engaged.
And he admitted the home side's winning margin should have been far more.
"We started the game very well - the scoreline at the end could have been the score after 20 minutes," Barrow said.
"In fairness to Bournemouth I thought they came into the game a bit before half-time and asked some questions.
"We sorted ourselves out at half-time, and I thought we were quite convincing in that second half.
"We've set some standards now and we've got to keep that going.
"We've had quite a few players out injured but we keep churning out performances and it's going okay."
The win extended Wigan's unbeaten domestic record under Rosler to seven matches.
But Barrow says no-one at the DW will be getting carried away just yet.
"I personally think there is more to come from us, which is a very positive sign," he said.
"We're not getting carried away, especially not under the gaffer - because he won't allow us to do that.
"He's very similar to Roberto Martinez in terms of work ethic, and I think everyone at the club appreciates that.
"The proof of the pudding is in the eating, and we are improving.
"But we know we have to carry on improving, and no-one here is getting carried away."