The hosts had controlled much of the game but failed to score at the Britannia Stadium as Hugo Rodallega headed home late on to ensure the Latics' Premier League status
Stoke City boss Tony Pulis bemoaned his side's lack of luck after they were beaten by Wigan at home, and hinted that his players eased up in the second half after controlling the first 45 minutes.
Hugo Rodallega's 78th minute goal meant the Latics remain in the Premier League, while the defeat was the Potters' first at home this calendar year.
The hosts were dominant throughout the first half but failed to get a goal before Wigan came back into the game in the second.
Pulis told reporters he was "really disappointed not to come in winning the game" at half-time.
"They rode their luck a little bit in certain areas," he said. "There were some generous decisions which also went their way, but I better be careful I don't [risk] the wrath of the FA."
The Stoke boss was, however, disappointed with his team's poor second half performance, believing his players took the foot off the gas and allowed Wigan to get back into the game.
He continued: "The first 20 minutes of the second half we were poor. We started as if the game was won and it was over, and Wigan were fighting for their lives.
"At the end of the day, we got some balls in the box but never looked like scoring in the second half.
"It's gone Wigan's way today and they rode their luck and good luck to them."