Northampton scored three first half goals to maintain their play-off bid.
Marc Richards robbed Mark Joseph to slam home the first, but Stuart Elliott swiftly equalised for Hull.
Eric Sabin claimed the second after Alton Thelwell's clearance struck him and ricocheted into the net, then added a third from Martin Smith's pass.
Hull's Andy Dawson celebrated his comeback with a fine free-kick before Stuart Green hit a post as they pressed for an equaliser late on.
Hull: Myhill, Hinds, Joseph, Delaney, Thelwell, France, Ashbee, Green, Elliott, Allsopp, Burgess. Subs: Musselwhite, Walters, Dawson, Lewis, Wiseman.
Northampton: Harper, Lyttle, Willmott, Reid, Sampson, Ullathorne, Trollope, Hargreaves, Smith, Richards, Sabin. Subs: Thompson, Westwood, Low, Asamoah, Taylor.
Referee: I Williamson (Berkshire)