In a match in which Villa were much the more clinical in front of goal, Calum Robinson opened the scoring on 39 minutes before Jack Grealish curled in a second just past the hour mark.
Rovers certainly had the chances against the NextGen champions but they couldn't find a way past Villa goalkeeper Benji Siegrist who made a series of fine second half saves to seal the win for the visitors.
On a chilly evening at Leigh Sports Village it was Rovers who were quick out of the blocks, Jordan Slew's goalbound shot on 6 minutes diverting off the head of Joshua Webb.
The home side continued to force the pace, Villa barely getting out of their half in the opening quarter hour as Rovers dominated.
But as the half wore on it was the visitors who started to impose themselves, Daniel Johnson racing through but firing wide with just Matty Urwin to beat served warning.
At the other end Tim Payne fired over from 25 yards but it was Urwin who was quickly called into action once more, saving well to deny Calum Robinson at his near post before Alfie Crooks headed over when well placed.
The deadlock was eventually broken on 39 minutes, Matty Urwin saved brilliantly when Johnson was played through, but seconds later another ball hit long saw Calum Robinson race into the area and he fired past the Rovers' 'keeper to open the scoring.
Rovers looked to respond straight away but John O'Sullivan saw his half-volley go straight into the arms of Villa stopper Benji Siegrist.
At the break Colin Hendry would have been delighted with how Rovers had started the game, but less so that the best chances had fallen to the visitors.
Rovers were strong starters once more as the second half got underway with strong claims for a penalty denied when Micah Evans was brought down in the area. Instead play was brought back to outside the box to where the resulting free kick saw Jamie Maclaren head over the bar.
Micah Evans just couldn't connect with a Maclaren through ball before a nice turn and shot from Osayamen Osawe flashed wide.
But despite Rovers enjoying the lionshare of possession it was the visitors who would once again create the bettter openings and there was none better than the 54th minute chance presented to Daniel Johnson who somehow failed to connect when a couple of yards out from a Jack Grealish pull back.
On 66 Grealish showed his captain how to finish with a second Villa goal that had been coming. The wideman cutting in from the left onto his right foot to curl a lovely shot into the far corner beyond the despairing dive of Urwin
The visitors continued to press Rovers back, Johnson twice firing wide of goal when other options were available.
Despite the scoreline and to their credit, Colin Hendry's side didn't give up, creating a host of chances as the game entered the latter stages.
Nuno Henrique headed over a John O'Sullivan free-kick before Jamie Maclaren's long-range strike failed to test.
Then Maclaren headed straight at Siegrist in the Villa goal on 78 minutes before the visiting 'keeper made a series of saves to prevent Rovers from getting on the scoresheet.
Siegrist somehow kept out a Nuno Henrique header from a Bradley Bauress free-kick, then from the resulting corner he saved from O'Sullivan and Maclaren in quick succession.
John O'Sullivan would be thwarted once more as the Villa man dived to his near post to save.
In added time Villa almost grabbed a third as Grealish squared for substitute Jordan Lyden but youngster Bradley Bauress blocked briliantly.
ROVERS: Urwin, Wylie, Bauress, Payne (sub Cotton 73 mins), Henrique, Daly (c), Osawe, Maclaren, Slew, O'Sullivan, Evans.
Subs not used: Dilo, Brown, Fernandez.
Booked: O'Sullivan, Nuno Henrique.
ASTON VILLA: Siegrist, Webb (sub Calder 87 mins), Lewis, Stieber, Donacien, Williams (sub Bateman 71 mins), Crooks (sub Lyden 81 mins), Carruthers, Robinson, Johnson (c), Grealish.
Subs not used: Watkins.
Goals: Robinson 39 mins, Grealish 66 mins.