A seventh-minute penalty from Rooney left a sour taste in the mouth after Villa old-boy Ashley Young theatrically milked Ciaran Clark’s contact, while Danny Welbeck tapped home from close range after Villa let a low Patrice Evra cross fizz across goal.
Villa escaped conceding a clear penalty when Nathan Baker handled, sweetening the Young row, which saw the visitors coaching staff complain to referee Mark Halsey at half-time.
Rooney - who had a mediocre game by his standards - struck a deflected third with Nani adding an injury-time fourth as United saw Villa off with ease in the end.
The result puts Sir Alex Ferguson’s defending champions on 82 points with four matches remaining, their next encounter against Everton before a derby with second-placed Manchester City at Eastlands.
Alex McLeish’s side lie on 35 points, six clear of the drop zone with five games to play.
The win comes as a welcome relief for Ferguson, who restored Paul Scholes to the starting line-up after he was rested for the shock 1-0 defeat to Wigan on Wednesday.
But question-marks were again raised over the conduct of Young, who went down in instalments after minimal contact from Clark, the second suspicious penalty he has won in consecutive weekends.
Villa - with Stiliyan Petrov watching from the stands after starting leukaemia treatment - started brightly enough, exciting young striker Andreas Weimann firing at David De Gea after a fine ball from Stephen Ireland. But United soon took control, passing well with Scholes running the show as Rooney had a goal-bound shot blocked by team-mate Young.
Young’s next intervention was none too pretty either - having done very well to skip away from Alan Hutton, he hurled himself to the turf in flamboyant fashion as Clark tried to back out of the challenge. There was the slightest initial contact, but Young made sure Mark Halsey pointed to the spot by sticking out his own trailing leg to ensure a theatrical fall.
A similar incident saw QPR’s Shaun Derry dismissed last weekend, with Young offside at the time, but on this occasion the card was yellow: like last week though, Rooney made no mistake with a low finish to the right.
United continued to press, Welbeck denied a close-range header by Nathan Baker’s fine block, with Given saving well from Rooney soon afterwards.
Villa had a rare half-chance as Clark headed a Barry Bannan free-kick wide, while Ireland curled a shot wide from range.
Normality was soon restored though as Scholes flashed a trademark volley from a corner just wide, while Given made a remarkable save to keep out Welbeck’s close range finish.
That wonder-stop was soon forgotten though, with Given sharing culpability for United’s second: the Irishman was joined by James Collins and Baker in leaving a low cross by Evra, the communication breakdown allowing a sliding Welbeck to ram home his ninth league goal of the season.
The second half saw Villa start brightly, although Hutton was fortunate to only see yellow for a wince-inducing late tackle on Young.
United were sitting back a touch, but De Gea was untested, and just after the hour mark the hosts cranked it up as they pushed to improve what could be a title-defining goal-difference.
They had a genuine penalty appeal waved away too, with Baker keeping his arms out as the Nani’s flick-on pinged up against him.
At the other end Emile Heskey - replacing the injured Clark - forced a decent save from De Gea with a trademark header, while Rooney missed a straightforward chance when he sidefooted wide after Valencia found him unmarked 12 yards out.
The England striker made up for it soon afterwards though as he completed a one-two with Valencia before ramming a low finish off the lunging Collins, the deflection leaving Given statuesque but - given the power and range - a goal likely anyway.
There were more chances for United, Given again making an unorthodox save from Welbeck via a heavy Collins deflection before denying Valencia’s also deflected shot, with substitute Dimitar Berbatov kept out by an Eric Lichaj block and Jonny Evans heading just over from the resultant corner.
Deep into stoppage time they got a fourth, Nani cheekily drilling past Given at the near post after a fine through-ball from Evans, the icing on the cake as United got back on track in style.