Gary Alexander's predatory first-half strike was enough to see off Northampton and send Millwall up to joint-third in the League One table.
Winger James Henry tormented the Cobblers - who sit three points above the drop zone - and he set up the only goal.
The on-loan Reading star beat Danny Jackman and his superb low cross left Alexander free to score from close in.
Henry headed a chance to make it 2-0 wide, while Northampton offered little.
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Millwall:
Forde, Frampton, Whitbread, Alexander (Grimes 90), Henry, Duffy (Barron 73), Craig, Martin, Laird (Harris 76), Abdou, Bolder. Subs Not Used: Pidgeley, Fuseini.
Goals: Alexander 35.
Northampton: Dunn, Crowe, Jackman, Hughes (Larkin 71), Doig, Magney, Coke, Constantine, Holt (Anya 55), Osman, Guttridge (Davis 55). Subs Not Used: Walker, Rodgers.
Att: 6,685
Ref: Grant Hegley (Hertfordshire).
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