U's midfielder Luke Berry opened the scoring in the 61st minute on Tuesday night before Shaun Harrad levelled things up two minutes later.
But Berry had the final word, notching an 86th-minute winner to book a second-round tie against Sheffield United on Sunday.
Jepson said: "I thought we created miles better chances in the second half.
"We hit the inside of a post with no-one getting to the rebound, we've had Jonah's (Craig Jones) header but we've been done at a corner.
"For their winning goal, it was Tom Soares' man - he was designated him at the set-piece and he hasn't gone with him and he's scored a goal.
"It was anyone's game before that and it was an open cup tie.
"I thought they had the better of it first half but we had the better of the second half until their second goal."