The Latics, who promotion from League One last season, travelled to their rivals requiring all three points to remain in the hunt for survival, and Shaun Maloney's side had been on course to achieve that desired result.
Young defender Charlie Hughes put the visitors in front with nine minutes remaining, with that scoreline putting the pressure on each of their opponents and Huddersfield Town, who play Cardiff on Sunday.
However, in the third minute of added-on time, Yakou Meite broke Wigan hearts, leaving the club three points adrift of safety but down due to Huddersfield and Reading still having to play each other on the final day of the season.
Despite earning a share of the spoils, Reading remain in the bottom three of the Championship standings with only their trip to the John Smith's Stadium to come on May 8.
Queens Park Rangers have secured their second-tier status for another 12 months after posting a 1-0 triumph at Stoke City, Albert Adomah netting the only goal of the game.
At the other end of the table, Coventry City beat Birmingham City by a 2-0 scoreline to move back into fifth position, and a win at Middlesbrough on the final day will seal a playoff spot.
While Sunderland came from two goals adrift to salvage a draw with Watford, Sunderland must beat Preston North End in their last game to have any chance of finishing inside the top six.
Preston and Swansea were the big losers of the afternoon as a 4-1 defeat for Preston at Sheffield United and Swansea drawing 1-1 at Hull City left it mathematically impossible to reach the playoffs.