A deflected Ryan Williams goal was enough to secure the Shrimps a first ever Football League win at the Pirelli Stadium after losing on their four previous visits.
And to complete a miserable afternoon for the hosts, defender Shane Cansdell-Sherriff was sent off in added time.
Rowett said: "I have to be honest and say I feel disappointed with the performance.
"We had an awful lot of the ball but we just didn't create enough. We didn't have a cutting edge and we didn't test them enough to win the game.
"I think a draw probably would have been a first result, but football isn't fair at times .
"We didn't get enough from the wide players and the strikers, which we have done in recent weeks.
"But I'm not going to complain too much because we're not going to win every game.
"We've done well for five or six games and have been top of the form chart, but we've just come off it a little bit here.
"It was a game between two competitive teams in difficult conditions but if I'm honest I don't think we defended well enough and I don't think we attacked well enough."
- Sports & Recreation