Uwe Rosler's side will now be in today's draw for the last eight following their win in south Wales.
Chris McCann put the Latics ahead in the first half with Fraizer Campbell levelling before the half hour mark.
But it was left to Ben Watson, the man who scored the only goal in last season's final victory over Manchester City, to settle the tie as he thrashed home a winner before the break.
Sunderland continued their transition into a fine cup team as Craig Gardner's stunning finish proved to be the difference as they saw off fellow Premier League side Southampton 1-0 at the Stadium of Light.
Sheffield Wednesday's fifth-round tie with Charlton was postponed due to a waterlogged pitch at Hillsborough, with both Sky Bet Championship sides going into the draw for the quarter-finals.