The Cobblers made a positive start and Ricky Holmes volleyed home when the ball fell to him following a corner.
County soon levelled as Thierry Audel nodded into the net after Adam Smith saved Liam Noble's initial effort.
Jon Stead put them in front from the spot after being bundled over, but Holmes was fouled at the other end and converted the game's second penalty.
Northampton, now unbeaten in 18 league games, need only three more points to guarantee a place in League One next season.
League Two leaders Northampton moved a step closer to promotion despite being held to a draw by Notts County.