By Dan Harrison at Hinckley
Gary Gardner struck with a stoppage time header to make it back-to-back draws for Villa's second string.
The claret and blues, who fielded first team trio Marc Albrighton, Ciaran Clark and Eric Lichaj, were left frustrated for much of this Bank Holiday Monday afternoon clash.
Despite creating the better chances, Kevin MacDonald's men found themselves trailing to a Calum McManaman goal six minutes before the break.
But Gardner bagged his first of the season in the dying moments to earn his side a well-deserved point at Hinckley.
The inclusion of Albrighton meant there was no shortage of attacking threat in the Villa starting XI and this showed early on as they dictated proceedings.
Wigan keeper Lee Nicholls made two key saves - firstly keeping out Graham Burke's powerful first-time drive and then brilliantly palming away a Samir Carruthers header from a Gardner cross.
But, on 39 minutes, McManaman slipped beyond the back line to collect Nouha Dicko's through ball and expertly slot past Benjamin Siegrist.
Skipper for the afternoon Clark thought he had levelled things on the stroke of half time, only to see his effort ruled out for offside.
The visitors had Nicholls to thank for keeping the scores level early in the second-half.
His superb one-handed save thwarted Albrighton whose curling effort seemed destined for the top corner.
Gardner and Carruthers both missed the target with close-range headers, while 18-year-old Carruthers went agonisingly close on two further occasions.
The former Arsenal trainee saw his 18-yard snap-shot trickle just wide of the post and he later struck the post from inside the six-yard box after a scramble in the Latics penalty area.
The waiting game paid off for Villa when Gardner shuffled across his marker in the second minute of injury time and sent a powerful header into the roof of the net from Albrighton's deep right wing cross.
Villa's reserves are back in action on Tuesday September 13 with an away clash against Everton at Finch Farm [ko 2pm].
VILLA: Siegrist, Lichaj, Williams, Clark, Lowry, Albrighton, Gardner, Johnson, Cameron, Carruthers, Burke. Subs: Taylor [for Burke, 83], Barrett, Caira, Nelson-Addy [for Carruthers, 86], Bryan.
WIGAN: Nicholls, Girvan, Mustoe, Robinson, Langley, Chow, Dicko, Breeze, McManaman, Dawson, Redmond. Subs: Cotterill, Rugg [for Dicko, 56], Astles, Boothman [for Breeze, 62], Watson [for Dawson, 86].