Cobblers are through to the next round of the EFL Trophy after Cambridge United could only manage a draw with Arsenal U21s before losing on penalties on Tuesday evening.
Cambridge had to win the match outright or triumph in a penalty shoot-out to keep alive their hopes and deny Northampton a place in the next round, at least until Colin Calderwood's side played Peterborough United next week.
But despite taking the lead at the Abbey Stadium, the U's were pegged back and then lost 4-3 in the shoot-out, Dan Jones missing the vital spot-kick when firing over the bar.
Harvey Knibbs had steered Cambridge ahead just before half-time but six minutes into the second-half United's Liam O'Neil picked up his second booking and was given his marching orders.
John Jules slammed home an equaliser nine minutes later before Arsenal triumphed on spot-kicks, despite missing their first attempt.
Earlier in the competition, Cobblers beat Arsenal U21st on penalties, lost 2-0 at home to Peterborough United and defeated Cambridge 1-0 at the Abbey Stadium thanks to Harry Smith's first-half goal.
Peterborough host Cambridge in the final match of Southern Group H next week but it is now confirmed that Cobblers finish second behind winners Posh, meaning Keith Curle's men face an away trip in the last 32 of the competition.
Ties are likely to be played in week commencing December 2 but details of the draw are yet to be confirmed.