A second-half double from Kal Naismith helped the Latics to victory after a Jack Butland own goal put them in front at the DW Stadium.
Story of the match
Latics deservedly in front
Wigan looked to pick up where they left off against Blackburn on June 27 and were almost in front after seven minutes when Jamal Lowe picked up the ball inside the area but fired wide at the near post.
Joe Williams then tried his luck from a free-kick just outside the area on 25 minutes as he curled towards the far corner, but Potters goalkeeper Butland was able to push it past the post.
The hosts continued to dominate in the first half and were rewarded five minutes before the break when Kieran Dowell drifted into the area and saw his low cross deflected in off of Butland.
Butland's horror show
Stoke looked to make amends for a lacklustre first-half performance after the break, but like many times before this season found themselves responsible for their own undoing.
After being initially challenged in the area by Shawcross, forward Lowe was first to the second ball and saw his close-range cross inexplicably fumbled by Butland and Naismith was there to nod the ball over the line.
Naismith wraps it up
Things then went from bad to worse in a matter of minutes for the Potters as Wigan grabbed a third.
Substitute Naismith cut inside onto his left just outside the area and fired past Butland into the far corner for his second of the night and pile more pressure on Stoke's bid for survival.
Man of the match: Jamal Lowe
The Latics forward was at the centre of most of his side's attacking play, providing the assist for Naismith's first, as well as posing a constant threat as Wigan targeted the Potters' weak left-side of defence. Unlucky not to get a goal of his own, also.
Wigan Atletic 3-0 Stoke City
Marshall, Byrne, Kipre, Balogun, Robinson, Morsy, Williams (Gelhardt, 89'), Dowell (Evans, 80') Jacobs (Naismith, 33'), Lowe (Massey, 80') Moore (Garner, 89')
Jones, Fox, Pearce, Mlakar
Butland, Collins (Smith, 70'), Shawcross (Chester, 70') Batth, Ward (Martins Indi, 70'), Cousins, Thompson (Gregory, 56') Ince (Campbell, 56'), Clucas, McClean, Vokes
Davies, Sorensen, Oakley-Boothe, Diouf
An almost perfect performance sees the Latics retain their 100 per cent record since the restart and move eight points clear of the relegation zone with six games to play.
The threat of relegation now looks to be a real possibility for the Potters.
Michael O'Neill's side face Barnsley in their next match on Saturday (July 4), and with games against Leeds United, Brentford and Nottingham Forest still to play, failure to win could see them face an almost-impossible escape.