O'Neill stormed on to the pitch at the full-time whistle to remonstrate with referee Mike Riley, who the Villa boss later claimed to have missed a foul on Ashley Young in the build-up to the winning goal.
He said after the match: "The officials also got three offside decisions wrong when we were clean through."
A statement on the FA's website confirmed that O'Neill has been charged for his behaviour at the final whistle, and not for his post-match comments.
The statement read: "The charge relates to O'Neill's conduct towards referee Mike Riley following the final whistle at Villa's match against Manchester United at Old Trafford on April 5."Aston Villa manager Martin O'Neill has been slapped with an improper conduct charge by the FA.