A first half goal from Jason Jarrett secured Wigan a place in the second round, but the 1-0 score line didn't reflect their superiority.
The Division Two leaders were too strong in all departments for Northampton, who, despite their second-half rally, failed to seriously threaten the Latics' goal.
But Town were aggrieved about the 31st minute goal which separated the two sides, as Andy Liddell appeared to have pulled back Duncan Spedding before feeding Jarrett, who went on to beat Nathan Abbey with a neat finish.
Wigan's hold on the game was such that defender Jason DeVos was able to join his colleagues at the other end and went close with a header in each half.
Abbey also saved bravely from record signing Nathan Ellington midway through the first-half and repeated the feat shortly after the restart to the deny substitute Neil Roberts. Top-scorer Liddell was also thwarted by a spectacular point-blank save in the second-half.
Northampton came into the game after the break, but were unable to break down a strong Wigan rear guard. Their only effort on goal came from a Daryl Burgess header which failed to trouble John Filan.
"I feel very aggrieved about the goal. Duncan Spedding was hauled to the ground by Andy Liddell and that cost us the game," said Northampton boss Kevin Broadhurst.
But Wigan boss Paul Jewell wasn't complaining: "It wasn't a great game but we deserved to win and defended relentlessly. Some decisions go for you and some go against you over the season."