Two goals in the space of three second-half minutes booked the League Two club, who had been dogged by financial troubles, a fifth round tie at Fulham on February 14.
Stephen Hunt, the former Southampton and Colchester defender, took advantage of poor Wigan marking from a 75th minute corner to break the deadlock before an own goal by Gary Caldwell completed a shocking night for Wigan, who supporters wisely decided to stay away in their thousands.
Those that did bother to turn up booed Roberto Martinez's side off the pitch at the final whistle, Wigan left to concentrate on staying out of the bottom three while Notts County's season remains very much alive.
Notts County, who started the evening as the lowest ranked team left in the competition, had come within seven minutes of knocking Wigan out at Meadow Lane 10 days ago.
And the basement division club once again made a mockery of the 59 places separating the two teams on the league ladder as they carved out the better chances after Jason Scotland had let them off the hook.
Scotland, who spurned a glorious chance to break his Premier League scoring duck in the 1-0 defeat to Everton last Saturday, was put clean through in the 11th minute but Kasper Schmeichel stood his ground to frustrate the Trinidad & Tobago international.
The lack of atmosphere did not help the Premier League club's cause as County grew in confidence the longer the tie remained goalless.
Lee Hughes and Ben Davies, who both scored in the original tie, were both denied by Vladimir Stojkovic in the space of four first half minutes while it required a clearance off the line by Scott Sinclair to prevent Neal Bishop from breaking the deadlock for the basement division club.
Sinclair was Wigan's most creative player, the on-loan winger from Chelsea making the most of his rare start.
After having a 46th goal-bound header clawed away by Schmeichel, Sinclair again went close before Martinez made a double substitution, Charles N'Zogbia and James McCarthy sent on in a desperate attempt to inject some urgency into his side.
But County got the breakthrough they so thoroughly deserved in the 75th minute, Hunt taking advantage of Wigan's static defence to head a corner past the despairing hands of Satojkovic.
And Wigan's problems doubled three minutes later, Caldwell putting past his own keeper while trying to make a clearance.
Wigan Athletic (4-5-1): Stojkovic; Boyce, Caldwell, Bramble, Figueroa; Sinclair, Scharner, Gomez, Diame (McCarthy 60), Koumas (N'Zogbia 60); Scotland. Subs: Pollitt, Amaya, Thomas, Watson, Rodallega.Notts County (4-5-1): Schmeichel; Thompson, Edwards, Hunt, Jackson; Westcarr, Ravenhill, Clapham, Bishop, Davies; Hughes. Subs: Hoult, Lee, Hamshaw, Fairclough, Hawley, Rodgers, Akinbiyi.Referee: Kevin Friend (Leicestershire)
FA Cup revised 5th round draw
Feb 13: Chelsea v Cardiff (12), Southampton v Portsmouth (12.30), Derby v Birmingham (3), Reading v West Bromwich (3), Manchester City v Stoke (5.15)Feb 14: Bolton v Tottenham or Leeds (1.30), Fulham v Notts County (3.00), Crystal Palace v Aston Villa (3.45).