Southend United face Crewe Alexandra in the semi-finals while Torquay United take on Cheltenham for the chance to play in the final at Wembley and join Swindon, Shrewsbury and Crawley in League One.
Northampton failed to record a victory against any of the play-off contenders, drawing five and losing three of their games.
Town boss Aidy Boothroyd meanwhile is hopeful that Clarke Carlisle will remain part of his squad for next season after the end of the experienced defender's loan spell at Sixfields.
"Conversations with Clarke are ongoing," he said after the weekend draw at Rotherham.
"I thanked all the loan players on Friday for the work they have done with us. Clarke will have a lot of offers and we’ve got to put an offer together for him and make sure all the little things that are important in his life are right for him."