Northampton went into the game level on points with Oxford United and Plymouth Argyle at the top of League Two but were behind within 9 minutes as Paul Benson opened the scoring for the home side.
John-Joe O'Toole returned to the Cobblers starting line-up, replacing Jason Taylor, after serving a one-match ban and he drew the visitors level in the 19th minute from a superbly worked free-kick routine, before Lawson D'Ath put Town in front on the half-hour mark.
Home manager John Still had been backed by opposite number Chris Wilder in the build-up to the game but the pressure on him was increased just before half-time when Marc Richards netted Northampton's third goal of the game.
Benson, with his second, and Danny Green with a penalty midway through the second half levelled things up as Luton roared back but the points were decided by substitute Ricky Holmes, capping a perfect day with his first goal since returning from injury.
Another superb performance from Wilder's men and they sit proudly at the top of League Two on Saturday night with Oxford United having been held at home by Carlisle and Plymouth Argyle beaten by Cambridge United.