Howe made 11 changes from the side which beat Huddersfield 4-0 on Saturday and his second string did not disappoint.
An unfortunate own-goal by Exeter captain Scot Bennett put the Cherries in front on 54 minutes before Dan Gosling crowned his full debut with the second 20 minutes later.
Exeter fought gamely but lacked quality in the final third, with Daryl Flahavan rarely tested in the visitors' goal.
"I was pleased with aspects of the performance," Howe said. "I thought we played some really good football in the first half and created a hatful.
"We should have been out of sight at half-time and funnily enough in the second half we weren't as good and won the half 2-0.
"We got better as the first half went on, we carved them open at times and if we had scored early on it would have been a lot easier night for us - but until we got that second goal it was always in the balance.
"There were some good patches and some stuff to work on as well. I had no hesitation on rotating the whole 11 regardless of the result on Saturday. I felt it was the right thing to do.
"We have such a strong squad that if you don't use it players become very frustrated very quickly. So I thought it was a good exercise.
"We work very hard on not conceding and that is something we need to keep working on because that wins you games."
Exeter manager Paul Tisdale was proud of his side's performance and rued the fact they did not take the one or two decent chances that came their way immediately after half-time.
"It was a really good game and a really good performance from Exeter City. I am very proud of them," he said.
"We defended very well and did very little wrong. We played a certain way today to give ourselves a chance of playing our game and we did that.
"We weathered a bit in the first half and opened up in the second, so it wasn't as if we were out of synch, everyone did their job.
"We lifted our attacking play in the second half and started getting forward more and we created a few good half-chances off the back of it.
"I think we were deserving of a goal tonight. I don't think anyone here will think we were totally dominated.
"They are a heck of a side and have a really strong squad. You only have to go through their side to see how strong they are and we did well to do as well as we did against them.