Jones struck after 20 minutes as United extended their unbeaten league run at Villa Park to 16 years.
Sir Alex Ferguson's side climbed back above Tottenham, who had briefly gone second with their win earlier this afternoon, and remained five points adrift of Manchester City after dominating for long periods.
The down side for the Red Devils was the early loss of striker Javier Hernandez with a serious-looking ankle injury, though they overcame his absence with relative ease.
Jones was given licence to go forward in midfield with Michael Carrick operating in the holding role, while Chris Smalling also did well in shackling Villa's most potent threat in Gabriel Agbonlahor for long periods.
Villa, meanwhile, confirmed winger Charles N'Zogbia had been left out of their match plans for an undisclosed breach of club discipline.
But they also suffered a double injury setback during the game with keeper Shay Given (leg) and Jermaine Jenas (ankle) both stretchered off.
Villa looked more threatening in the second period but could have no complaints with the outcome.
United winger Ashley Young was greeted with boos from some sections of the home fans on his return to Villa Park.
United suffered an early setback when Hernandez appeared to twist his ankle when it became caught in the Villa Park surface after turning sharply.
There was a lengthy delay while Hernandez received treatment but he was unable to continue and was stretchered off and replaced by Antonio Valencia.
It came as no surprise when Jones put United ahead with a clinical finish after 20 minutes.
Patrice Evra released the overlapping Nani and his cross was met by Jones who volleyed past Given from close range.
Villa could not get a foothold in the game and it needed a fine save from Given to prevent United doubling their lead.
Young provided the probing cross from the right of the area and Nani's powerful header was turned aside by the Republic of Ireland keeper.
There was a brief moment of danger from Villa when Barry Bannan ran on to a reverse ball from Agbonlahor inside the United box but he over-ran the ball.
But United were the dominant force and Antonio Valencia curled a 25-yard effort just wide after no-one had closed him down.
Given had to be replaced by Brad Guzan after 38 minutes after hurting his leg when racing out of his area to clear.
The second period began in the same vein as the opening 45 minutes with United dominating proceedings.
Wayne Rooney tried his luck from 25 yards out and his shot skidded just past the post.
Then Bannan made a crucial block on Nani's shot from near the penalty area, then Anders Lindegaard clung onto a teasing cross-shot from Agbonlahor in a rare Villa attack.
Jenas became the third player to be substituted after 64 minutes with a serious-looking ankle injury and he also had to be stretchered off.
Villa substitute Emile Heskey almost made an instant impact as he headed wide at the far post after Richard Dunne had flicked on a corner from Bannan.
Young dragged a low 20-yard effort only a couple of feet wide after brushing off the challenge of Bannan.
But Villa were at last showing some menace with Lindegaard turning over a Collins header from a Dunne centre.
Young curled a sot straight at Guzan after good play by Ryan Giggs but could not score against his former team-mates before being substituted after 78 minutes.
Rooney had a quiet afternoon but was just too high with a snap shot after exchanging passes with Carrick.
Substitute Danny Welbeck had the ball in the net in the 90th minute but had strayed offside.