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The Cobblers eased into a two-goal lead and despite Mamady Sidibe's second-half goal it proved to be mere consolation for the hosts.
Northampton almost took the lead in the fourth minute when a Richard Rose clearance fell to Scott McGleish who fired well wide of the target.
Pedj Bojic then forced Jason Brown into a good save following neat build-up play by the visitors.
Matthew Jarvis then shot wide from a tight angle before Marc Richards went close at the other end.
Northampton stunned the Gills when they took the lead in the 32nd minute.
Both Alan Pouton and Richard Rose missed challenges to allow Eric Sabin to slot the ball past Jason Brown.
Four minutes before the break David Galbraith crossed from the left to Josh Low at the back post and he laid the ball into McGleish's path who made it 2-0.
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Sidibe headed a late chance wide but it was the visitors who deserved their victory and a place in the second round.