The table-topping Gills, beaten for the first time by Rochdale on Saturday, maintained their 100% record on the road with a 2-1 success at Sixfields.
Goals in either half from Deon Burton and Jack Payne saw Allen's side pick up three more points despite Adebayo Akinfenwa pulling one back for the hosts late on. The only sour note for the Kent club was the dismissal of Charlie Allen in stoppage time after picking up his second yellow card.
"That was a fantastic performance," said Allen, whose side are now five points clear at the summit. "It's a difficult place to come, Northampton put long throws in from either side of the pitch and you have to battle here.
"We set out to get the ball down and play in the first half but it was backs to the wall in the second half and every single player did their bit. We knew the ball would be around our box in the second half but everyone stood up to the challenge.
"Deon Burton's finish was excellent and Jack Payne has got two goals from that position now and it was another superb technical finish. He deserved to get a goal like that with his hard work. I thought he might need a few more days of training but in the end I decided to play him."