Javier Hernandez was stretchered off within the first 10 minutes as the young defender registered the only strike in a game dominated by Sir Alex Ferguson's visitors.
Not everything went the Red Devils' way in a muted match, however, with striker Javier Hernandez being forced off on a stretcher within the opening 10 minutes having appeared to twist his ankle.
Jones' strike came after 20 minutes with an impressive finish at the end of an athletic run into the box, where he met Nani's cross from the left.
An early blow came for United when Hernandez went down in the box having appeared to twist his ankle nastily. He immediately signaled to be withdrawn and was replaced by Antonio Valencia in a tactical reshuffle which saw Nani move into a central role behind Rooney.
But United still dominated the opening 20 minutes without finding much quality in the final third. Eventually Villa lost sight of Patrice Evra in the space in front of the back four. With all the time in the world, the Frenchman slipped Nani through down the left where he delivered a simple cross. Jones made a run into the box and poked home left-footed for the first goal of his senior career.
In a rare opportunity inside the away half, Gabriel Agbonlahor showed some threat cutting in from the left flank and jabbing a smart pass into Barry Bannan, but the Scot’s first touch saw him carry it too far wide.
More bad news arrived for Villa as the first half came to a close when Shay Given, having rushed out to scramble a clearance, was forced off with an apparent hamstring problem, necessitating the introduction of Brad Guzan for his second Premier League appearance.
Ten minutes into a sedate second half, Stephen Warnock shut down a potentially dangerous United move when he expertly slid in to rob Rooney on the edge of the area.
There followed yet another sudden injury when Jermaine Jenas, only making his first start for Villa since arriving from Tottenham in the summer, appeared to trip over something in the pitch and was also stretchered off.
His replacement, Emile Heskey, seemed to give the home side another option going forward, being targeted immediately from a corner. The former England striker was found at the far post after Richard Dunne flicked a header on but he nodded high to waste a decent chance.
Young responded for the visiting side by cutting inside from the left wing and slicing a long-range effort low and just wide of Guzan’s near post.
Finally, with 15 minutes remaining, Villa forced Lindegaard to make a save. James Collins headed powerfully towards the top corner from a corner only to be denied by the leaping Dane.
Late substitute Danny Welbeck nearly lit up the turgid second half as he beat three home defenders in a skilful, weaving run into the penalty area. Unfortunately for the Manchester United striker, though, he could not quite skip past the final man at the post and lost the ball.
Rooney then had a chance to finish the game as he careered forward on the break and bore down on the Villa area, but he opted to pass into the path of Welbeck, who put the ball in the net but was comfortably offside.