Jamie Robson's unfortunate own-goal proved the difference as Latics were beaten at Accrington.
Latics, who were unbeaten in four going into the fixture, created more of the chances but Robson's 31st-minute own goal settled the tie.
The visitors got off to the better start, with Kai Payne testing Stanley goalkeeper Ollie Wright and Josh Hawkes trying his luck with two long-range efforts which were just over the bar.
However, Stanley took the lead following their first real attack after 31 minutes.
A Shaun Whalley free-kick found Benn Ward, whose shot was pushed out by keeper Mat Hudson on to his Latics team-mate Robson and the ball rebounded in via the post.
Isaac Heath then fired just wide for Stanley, then in first-half stoppage time, Kane Drummond was clean through for the Latics but was denied by the legs of Wright.
After the break, chances were at a premium but Latics sub Michael Mellon had three strikes on goal, two just wide and one saved by Wright.
Latics gaffer Micky Mellon said: “We lacked that bit of guile and bit of quality and we gave away a soft goal, and we’re not happy about that.”
