Furious Millwall fans booed their team off the pitch after seeing them slump to a second home league loss in a row.
The Lions dominated the early stages and Chris Zebroski saw an early effort scrambled off the line and also hit the post with a shot from a tight angle.
Zoumana Bakayogo also wasted two decent chances but the Cobblers took the lead when Mitchell Cole volleyed home.
The Lions created further chances but Alan Dunne, Marvin Elliott and Danny Senda all failed to trouble the keeper.
Millwall: Pidgeley, Ross, Robinson, Shaw, Whitbread (Senda 75), Dunne, Elliott, Fuseini, Bakayogo (Grant 59), Braniff (Hubertz 45), Zebroski.
Subs Not Used: Day, McInnes.
Northampton: Bunn, Chambers, Dyche, Doig (Hunt 45), Crowe, Bojic (Quinn 83), Taylor, Jess, Cole (Watt 60), Kirk, McGleish.
Subs Not Used: Harper, Gilligan.
Goals: Cole 42.
Ref: P Melin (Surrey).