First-half goals by Lee Hughes and Ben Davies had put the League Two side into dreamland at a bouncing Meadow Lane.
Jason Scotland pulled a goal back for the Latics in a second half where both sides created several chances.
Wigan were gifted a chance in the 24th minute when a mistake by Jamie Clapham let in Jordi Gomez, who found Hugo Rodallega and the Colombian's shot was turned onto the post by Kasper Schmeichel.
Two minutes later and Hughes raised the roof.
A fine pass by Davies put him in behind the defence and he held off Antonio Amaya and finished calmly underneath the keeper.
Wigan were clearly rattled and after a foul by Titus Bramble on Hughes, they were punished by a magnificent free-kick from Davies that bent over the wall and nestled in the bottom left-hand corner.
James McCarthy nearly pulled a goal back for the Latics just before half-time but his shot came back off the near post.
But Wigan were back in business when a neat throughball by Rodallega put Scotland in the clear and he knocked it past Schmeichel to finally claim his first goal for the club.
The visitors were now a renewed threat and Scotland came close again by whipping a shot just wide of the post then forced a save by Schmeichel at his near post.
Luke Rodgers was immediately part of the action after coming on when he forced a good save by Vladimir Stojkovic as the Magpies threatened again.
But Wigan's pressure paid off with seven minutes left when Charles N'Zogbia's corner was headed across by Bramble and Watson had the simple task of nodding it in.