It means Villa have now beaten United, Liverpool and Chelsea this season but O'Neill was wary of reading too much into the result.
"This win will give us a great deal of confidence but that could quickly be eroded at Sunderland on Tuesday," he said.
"It is a really great win, and I am not trying to play it down, but the main thing is the players should be really delighted with their performances against sides that they normally find it hard against."
Even Sir Alex Ferguson admitted Villa had edged the first half, but he was irritated at the amount of time added on by referee Martin Atkinson, who decided three minutes was enough for six substitutions and two lengthy injury stoppages.
"The timing should be taken out of the referee's hands," Ferguson said. "Those two stoppages took two minutes and 20 seconds, and then there were the substitutions on top of that. That is disappointing.
"It is silly really. We are nearly in 2010. A change should be made."
That Ferguson should be complaining about such things told its own story and the United boss was overstating the situation somewhat when he stated his side "pummelled" Villa after the interval.
In fact their best chance came before the break when Wayne Rooney smashed a shot against the bar.
Nemanja Vidic had a second-half header booted off the line by Stewart Downing and Brad Friedel made a smart save to deny Dimitar Berbatov late on.
But the Bulgarian failed to make proper contact after he had been set up by Michael Carrick and it was a poor return for a United side losing for the fourth time this term.
"It is a missed opportunity," Ferguson added. "We created plenty of opportunities and we should have taken at least one.
"But this is not an easy league. If you get there, you are going to be taken the distance. As I always say, if we are in touching distance on New Year's Day we won't be far away."
After being in the top four for so long last year only to fade dramatically at the end, O'Neill is right to be cautious this time around.
However, he has a fine squad of players at his disposal, Downing available after a long-term injury and James Milner producing fine performances in central midfield.
"If it has done nothing else it will stop people asking about our record here," added O'Neill, who also revealed Stephen Warnock is unlikely to be fit for Tuesday after suffering whiplash during a collision with Park Ji-sung.