United trailed by a 19th minute strike from Gareth Barry and it was only after the introduction of Ruud van Nistelrooy and Roy Keane that Sir Alex Ferguson's side moved into a matchwinning mode.
One man who must have been impressed with Scholes' goalscoring exploits was the watching England coach, Sven Goran Eriksson.
Villa, who enjoyed several good spells, were disappointed to lose their first game in six matches.
United, who made five changes, were indebted to an early save from Tim Howard when the American saved a close-range shot from Juan Pablo Angel following a right-wing cross from the recently rejuvenated Darius Vassell.
Howard again came to United's rescue when he kept out a Vassell shot with his legs as Villa were exposing United's sluggish defence.
But Howard had little chance when he was completely wrong-footed by a shot from Barry which was deflected into the net off Wes Brown.
The referee, to his credit, allowed the advantage after John O'Shea fouled Angel. The ball ran into the path of Barry to notch his third goal of the season.
United came to life after this goal and it was Villa's turn to enjoy some good fortune when an O'Shea header from Ryan Giggs' corner was pushed onto the bar by Thomas Sorensen and from the rebound Mikael Silvestre's shot was blocked.
Ten minutes into the second half Ferguson sent on his big guns, van Nistelrooy and Keane but there was no immediate improvement as it was Villa who picked up their game to give glimpses of their first-half display.
But in the 64th minute United finally got on level terms. Angel lost possession in midfield and the ball was played down the right to Giggs who cleverly pulled
his pass back into the middle for Scholes to tap home his sixth goal of the season.
Four minutes later the Giggs-Scholes combination resulted in a second goal which put United into the fourth round.
Giggs sent over a right-wing cross which Scholes swept confidently past Sorensen.