The champions could have gone level with Chelsea at the top of the Premier League after the leaders were held 3-3 at home by Everton but instead suffered a first home defeat by Villa since 1983 after failing to reply to Gabriel Agbonlahor's header.
"We were camped in their box for a lot of the second half and had some really good chances," Ferguson told MUTV.
"We only needed to take one to get us back in the game and it might have changed from then on; it was just one of those days when it wouldn't go in.
"I think we deserved something from our second half showing. There wasn't much in it in the first half and there were chances at both ends. They probably just shaded it and deserved the goal. But we pummelled them after half-time and had a lot of good opportunities but didn't take any."
Ferguson was angered by the amount of stoppage time added on at the end, but praised Villa who moved into third place.
"Their defenders worked their socks off and they deserve full credit for that," Ferguson added. "They were closing down players, blocking shots... doing everything they could. It was a big strong effort by them."
United have now lost four league games, but Fergsuon believes the nature of the title race this season means that they are still well-placed to retain their title.
"It's not an easy league. I say that time and time again. If we get to January within touching distance of the leaders then we're in with a great chance," he said.
Villa have now beaten United and Liverpool away this season and Chelsea at home.
"Our record against the top four this season has been exceptional," manager Martin O'Neill told the BBC. "I thought we played intelligently and courageously. It has been a long time since this football club won at Old Trafford."
Asked about his angry reaction when only three minutes were added on, Ferguson called for timing in matches to be taken out of the hands of the referee.
"You get to the point on adding time on, it should be taken out of the referee's hands," he said.
"There were two stoppages of two minutes three seconds and we played three minutes (stoppage time)," he said.
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