Jason Pearce scored the winning goal on his debut for the club with the Latics enduring a tortuous eleven minutes of stoppage time at the end of the game.
The only black mark on the evening was the injury to Chris Herd which looks set to rule the Aston Villa loanee out for the remainder of the season.
Steve Clarke however wasn't too impressed with his side. "A little bit of me is embarrassed to be coach of a team that plays like that,” he said. “Especially first half. It wasn't a good game, not a good performance and obviously a terrible result.
"We didn't turn up for the first half, we allowed Wigan to get in front and the second half was a consequence of the first half performance, not acceptable."
"The players ran around, they put everything into the game but they didn't put any quality in the game. Look at the quality of the last two home games, not just from us but the overall quality.”
The result leaves Reading in the relegation battle, seven points above the relegation places.