Burton-born full-back Dean Howell scored direct from a free-kick in the 47th minute to give the newly-promoted Cod Army their first-ever win in the Football League.
"We never really got going that's the most disappointing aspect, but the boys have done well so far this season so I'm not going to criticise too much," said Rowett.
"We never really played with the same intensity as we did against Wimbledon. It was a little bit of a case of after the Lord Mayor's Show from our point of view unfortunately.
"We knew it would be a different game and we knew they would sit in there and try to catch us on the break. We did have opportunities in the first half and late on in the second half but the finishing wasn't there on this occasion.
"I think you have to hold your hands up and say that they defended resolutely and did what they needed to do to win away from home."
