Marcus Stewart scored after just three minutes from a Liam Lawrence cross, but Wigan's players claimed the ball had gone out of play in the build-up.
Wigan pushed for an equaliser but struggled to create clear-cut chances against a resolute Sunderland defence, cheered on by 7,500 visiting fans.
Sunderland boss Mick McCarthy:
"The goal happened right in front of me and I didn't think it had gone out.
"I was screaming at Liam Lawrence to play on and he put over a fantastic ball which Marcus finished off.
"The truth is Alan Mahon should not have stopped. You tell every schoolboy to play to the whistle. That is what I was taught as a kid."
Wigan: Filan, Eaden, Jackson, Breckin, Baines, Teale (Jarrett 64), Kavanagh, Bullard, Mahon (Ormerod 45), Roberts, Ellington.
Subs Not Used: Walsh, McMillan, Wright.
Sunderland: Myhre, Wright, Breen, Caldwell, McCartney (Danny Collins 73), Robinson, Lawrence, Whitehead, Arca, Brown, Stewart (Elliott 82).
Subs Not Used: Deane, Thornton, Alnwick.
Goals: Stewart 3.
Ref: A Marriner (W Midlands).