Both sides have made slow starts to the season but the Pilgrims gained a vital win at Mansfield in their last outing to ease the pressure on manager John Sheridan and he named an unchanged side for the game.
Opposite number Aidy Boothroyd was given the full backing of Cobblers chairman David Cardoza in midweek and also drafted in midfielder Kane Ferdinand on loan from Peterborough United who was handed his debut alongside fellow loanees Stuart Dallas and Luke Norris.
1st Half: Despite Trevor Kettle being in charge the game failed to come to the boil in a scrappy opening 45 minutes of few chances, a situation that probably suited the visitors more than the home side.
2nd Half: Plymouth upped the tempo after the break but couldn't find a way through until, heartbreakingly for Northampton, Lewis Alessandra netted in the final minute of normal time.
More late agony for Boothroyd and his side who now lie at the foot of the League Two table.