United and Villa were labouring towards a goalless draw until Rooney was introduced 20 minutes from time.
The striker's arrival revived the visitors and after taking the lead with Cristiano Ronaldo's 19th goal of the campaign, Rooney finished Villa off with a well-taken strike late on.
"I have been trying to find a new Ole Gunnar Solskjaer as a substitute - although I don't think Wayne would appreciate that," laughed Ferguson.
"Wayne changed the game when he came on. He brought us thrust and enthusiasm and direct play. He attacked defenders and made a heck of a difference to the game."
It ensured an 11th straight win at Villa Park for Sir Alex Ferguson and a 13th successive victory over Villa for United.
"It is difficult to say why we have such a good record here," said Ferguson.
"It is a traditional, old-fashioned football ground. The fans are right on top of you and there is always a good atmosphere."
After clarifying his feelings about the lack of atmosphere at Old Trafford during the New Year's Day win over Birmingham on Friday, Ferguson also reinforced his belief United's travelling fans are among the best.
"We had 7,500 fans here, who had a real party," he said.
"Every time we come to Aston Villa, they are really up for it. They can make a difference, which is the point I made last week.
"When our fans are like that, we do not let them down."