The League Two side gave themselves a two goal cushion going into the break with goals from leading goalscorer Lee Hughes and Ben Davies the difference between the two sides.
Roberto Martinez’ largely changed starting line up looked out of shape to put it lightly.
The Wigan manager made no fewer than six changes to his side with a debut for Serbian keeper Vladimir Stojkovic and both Paul Scharner and captain Mario Melchiot both rested with a swollen ankle and broken nose respectively.
Hendry Thomas missed out through suspension thanks to his red card at Wolves last time out and Gary Caldwell and Charles N’Zogbia resigned to the bench.
Jason Scotland started up front with Hugo Rodallega moving out to the wing and Scott Sinclair, making his fourth start of the campaign, took up the opposite flank.
Notts County took the game to their Premier League guests and with Lee Hughes a constant threat up front it came as little surprise when the controversial former West Brom striker put them in the lead with 25 minutes on the clock.
The County number nine barged his way past Amaya with relative ease before planting the ball past Stojkovic.
That was Hughes’ 20th goals for County since his move from Oldham last summer and the 34-year-old was certainly up for adding to that tally as he continually tormented the Wigan defence with Spaniard Antonio Amaya the main victim.
Amaya, making only his third appearance in a first team shirt, was having the kind of afternoon that he will probably want to forget.
And during the latter stages of the first half Amaya switched positions with Titus Bramble in the hope that the skipper for the day would have more luck in dealing with Hughes.
However it was Bramble’s foul on Hughes 20 yards out that inadvertantly led to the home side’s second goal with Ben Davies striking home the resultant free kick with aplomb.
James McCarthy almost made it three goals in three games but for the width of the upright as the opening half came to a close.
That effort from the youngster and a Hugo Rodallega effort midway through the first half that keeper Kasper Schmeichel did well to finger tip onto the post were virtually all that Latics had to show from a dismal 45 minutes.
Ivory Coast Steven Gohouri international took to the field for the second half making his debut for Wigan as replacement for the ineffective Amaya.
The second period began pretty much as the first had been played out and if it hadn’t been for Stojkovic’s superb fingertip save to deny Hughes early on Wigan would have been on their way out of the cup.
That save proved crucial as minutes later Jason Scotland pulled one back combining with Rodallega to fire past Schmeichel from the edge of the area for his first Wigan goal at the 21st attempt.
The Trinidad & Tobago striker almost added a second with a decent effort from outside the box shortly after and then was thwarted by Schmeichel from close range.
Wigan weren’t having it all their own way however and had Stojkovic to thank on more than one occasion with Hughes and Luke Rodgers, once a target for Wigan, both denied by the on loan keeper.
The introduction of Charles N’Zogbia in the 70th minute gave Latics more impetus and it was the French winger’s corner that led to the equaliser.
Titus Bramble rose to meet the flag kick and nodded it down for Ben Watson, also a 70th minute substition, to head home from close range.
Wigan were again grateful to Stojkovic when he managed to pull off another fingertip save after Johnnie Jackson’s corner deflected off Mohamed Diame and threatend to deny them a place in the Fifth Round draw at the death.
The two sides will now do it all again with the replay scheduled for Tuesday February 2nd.