The Terriers could have climbed up to fourth place with victory, though a run of one win in their last seven leaves them at risk of slumping down the table unless fortunes change fast.
A second defeat to a side at the bottom end of the table in the space of nine days may be a massive blow to Town's hopes of promotion, but for Wigan they are now up to 22nd and only inside the relegation zone on goal difference.
Wigan slowly started to grow into things and so nearly made the breakthrough at the end of a Yanic Wildschut shot, which trickled wide of the target, seconds after the Terriers had a goal ruled out for offside.
Van La Parra and Sean Scannell both had chances to make the difference, with veteran stopper Jussi Jaaskelainen finding himself in the right place, while up the other end Danny Ward had to keep out a Wildschut drive.
The breakthrough did arrive prior to the break, though, and it was Reece Burke who grabbed it by finishing off Wildschut's run - his first goal for the Latics.
Huddersfield, who lost a couple of players to injury before the interval - including skipper Mark Hudson inside the opening 10 minutes - battled back well and were all square when an unmarked Mooy was picked out by Nakhi Wells.
Wildschut was proving to be the best player on the field, constantly causing problems for the hosts and making a telling difference on the hour when charging half the length of the field on the break and calmly rolling the ball home.
The same player perhaps should have put distance between the sides moments later, only to fluff his lines when one on one, and it was nearly a big moment in the match as Wells went down inside the box and felt that he should have had a penalty.
It was not to be on that occasion, with matters only made worse for Town as Kachunga also saw his appeals waved away, leaving the home side on the brink of another setback.
Max Power tested Ward late on with a decent attempt, and that ultimately proved to be it as Wigan picked up three precious points in their battle to avoid the drop.