The hosts dominated large spells of the game but were unable to break the deadlock in the Group D encounter at the Jan Breydelstadion.
Wigan manager Owen Coyle made seven changes to the side that lost 2-0 to Leicester City in their last Championship game, with the likes of Marc-Antoine Fortune, Jean Beausejour and Roger Espinoza all left out.
Coyle also opted to rest in-form forward Shaun Maloney in favour of former Sunderland man James McClean.
His Zulte-Waregem counterpart Francky Dury, meanwhile, decided to stick with 10 of the side that lost their last Belgian Pro League fixture 5-2 to Genk, with the injured Steve Colpaert making way for Bernard Malanda Adje.
Wigan made the better start to the game, with James McArthur seeing his shot from outside the box glance the post in just the second minute.
The home side then had a good chance to open the scoring though, Wigan keeper Scott Carson saving well from Ibrahima Conte.
And the visitors again had Carson to thank for keeping them level going into the break, as the England international thwarted both Thorgan Hazard and Conte for a second time with excellent stops.
Dury’s men continued to pressurise Wigan after the interval, with Mouhamadou Habibou only able to head wide after getting on the end of a brilliant cross from Davy De Fauw just minutes after the restart.
That effort was followed up shortly after by a shot from Conte as Carson was again called into action, but Wigan then went close themselves as Zulte-Waregem keeper Sammy Bossut to pulled off a brilliant save from James Perch's effort.
That proved to be the visitors only chance of note for the remainder of the game, as the hosts piled forward in search of a winner.
However, they found Carson in inspired form and the referee unwilling to listen to their appeals for a penalty after a Hazard shot struck Ryan Shotton as Coyle's side held on to claim a valuable point.
