The League One side continued their excellent recent run with a 3-0 success at Sixfields to make it seven straight wins in all competitions.
Aidy Boothroyd was unhappy with a number of decisions made by the match officials and also felt his side had been on top for the first 45 minutes.
“We were by far the better team in the first half," he said.
O's assistant boss Kevin Nugent felt, however, that the visitors had turned in a very professional display.
"It was a really tough game tonight," he said.
"They were tough conditions. It was very cold and windy but I thought it was a fantastic performance over the 90 minutes."
Northampton return to league action this Saturday when they face Cheltenham.
Source: Cobblers Mad