The FA Cup semi-finalists kept their dream of an instant return to the Premier League well and truly alive - while inflicting a massive dent in Ipswich's own promotion hopes.
Tommy Smith had given the home side the lead, but it lasted little over two minutes as James McClean equalised before Leon Barnett put Wigan ahead at the interval.
McClean made the points safe in the 76th minute, finishing off a well-worked move, to round off a great week for Uwe Rosler's men.
Ipswich made a strong start, having the first chance when Paul Anderson rose well to meet Stephen Hunt's free kick but the powerful header went narrowly over the crossbar.
Ipswich shaded the opening exchanges and Wigan keeper Ali Al-Habsi had to scurry down to his left to deny Daryl Murphy's scuffed attempt after Aaron Cresswell and Paul Anderson had combined on the left.
And the home side took a deserved lead in the 19th minute when Wigan were twice unable to clear their lines and Smith met Cole Skuse's header back in to divert the ball past the diving Al-Habsi.
But the lead lasted just 127 seconds. Emmerson Boyce released Marc-Antoine Fortune down the right and his low cross was met with clinical precision by McClean who fired the ball low past Dean Gerken.
Ipswich continued to shade the better chances and they should have taken the lead in the 39th minute.
Aaron Cresswell's low cross was expertly teed-up by Paul Anderson but Luke Hyam fired over from 10 yards.
But it was the visitors who went in at the break ahead after some horror-show defending from Ipswich three minutes before the interval.
Jordi Gomez' free kick was met by the unmarked Barnett and the former Norwich man had the simple task of heading past Gerken.
Wigan were forced to show their qualities at the other end straight after the restart as Ipswich looked to force an early equaliser.
But it was the in-form visitors who spurned a golden chance to extend their lead when they found themselves in a three-on-one situation but the one, Town left-back Cresswell, made a last-ditch tackle.
Wigan's quality eventually told when Paul Green was dispossessed by man-of-the-match Gomez who fed Fortune.
The big striker had the presence of mind to roll the ball to the far post where McClean had the simple task of making it 3-1.
Ipswich responded well with subs Sylvan Ebanks-Blake and Paul Taylor going close, the latter forcing a smart stop of Al-Habsi at his near post but it was all to no avail.