The away side came closest to opening the scoring after nine minutes when Tim Cahill fired an effort from distance, but it drifted just wide.
Everton again went close moments later when Denis Stracqualursi found a powerful strike inside the area, but Ali Al-Habsi was more than equal to the effort.
The returning Steven Pienaar went close for Everton after 30 minutes with a strike from distance, before Darron Gibson, fresh from his strike against Manchester City, fired wide moments before the break.
Everton introduced Nikica Jelavic early in the second period in an attempt to inject some ideas into their forward line, but it was Wigan who found the opener after 77 minutes.
The Latics were given a helping hand after a horror show from Howard, who allowed the ball to slip through his grasp after it had struck Phil Neville.
Wigan will look to return to winning ways when they travel to Bolton next weekend, while Everton host Chelsea.