Needing victory to move level at the top with Chelsea, Gabriel Agbonlahor's first-half effort instead left United three points adrift.
Villa are now in third, as they added the Red Devils to the scalps of Chelsea and Liverpool which have already been collected in another fine campaign.
"Second half I think we deserved something," Ferguson told ESPN.
"There wasn't much in it first half, they probably just shaded it and deserved the goal.
"Second half we pummelled them, had a lot of good chances and didn't get any.
"It's just one of those days it wasn't going in."
Ferguson was aggrieved, once again, at the lack of stoppage time and believes time-keeping should no longer be the referee's responsibility.
"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)."
Ferguson does not believe the defeat, coming after Chelsea drew 3-3 with Everton on Saturday afternoon, hampers United's title chances too greatly.
He added: "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."
Man of the match Agbonlahor praised Aston Villa's team ethic.
"Previous seasons we've come here and gone in front they've come back and beaten us," Agbonlahor told ESPN.
"We're keeping clean sheets, so it's down to the defence.
"We worked hard for each other out there, all 11 players defending for the team and got the result."
Captain Richard Dunne, who joined Villa from Manchester City last summer, was thrilled.
"I think we deserved it," he said.
"We don't know any other way to play, we like to get it down and try and attack.
"Second half, as much as we like to attack, there was too much defending to be done.
"It was quite difficult but it was another performance where we can be pleased with ourselves."