Play-off chasing Tranmere were made to pay for missing several good chances as Northampton salvaged a point.
Charlie Barnett hit the post for Rovers before Bas Savage heading the visitors in front from Danny Mayor's pass.
Ian Moore wasted a great opportunity to double the lead after Mayor and Barnett combined to put him in good position.
Andy Holt levelled after Colin Larkin's strong run and good approach play from Ikechi Anya. Cobblers keeper Chris Dunn tipped Moore's header over late on.
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