Nolan had few complaints about the result and called on the Trotters squad to regroup for the weekend league clash with West Bromwich Albion.
"It was a disastrous result for us really, but fair play to Northampton because they came here, set their stall out and made it difficult for us," he said.
"We've spoke after the game and we can't be happy with that performance. We know as players that we have let ourselves down as well as the gaffer, the staff and the fans.
"This was a massive chance for us to go on and do something outside the Premier League and maybe get into Europe through this route.
"But it wasn't to be and now it's all our attention to the league because that's all we have got until the end of December."