The Cobblers' nerves were jangling throughout as they knew that any failure to put away Harriers and a victory for Darlington would see them miss out.
They were unable to convert any off their first-half chances, with Kirk the main culprit.
But the former Boston man came up trumps with his seventh goal in eight matches since making the switch, taking his season's tally for both clubs to 27.
Kirk broke the deadlock in the 67th minute when he fired past debut goalkeeper Daniel Lewis, who had performed wonders to keep out Fred Murray's initial volley and the first rebound attempt by Kirk.
Any hopes Harriers had of clawing a result at Sixfields as they bade farewell to the League after their five-year stay, were shattered when they had John McGrath sent off 16 minutes from time after a centre circle flare-up which involved most of the 22 players.
Northampton then ran their visitors ragged in the closing stages, with substitute Eric Sabin proving the tormentor in chief.
With five minutes remaining Sabin pulled back a cross for Low to tuck in Northampton's second and two minutes later Sabin popped up down the left before squaring the centre for Low to convert his second.
The victory booked the Cobblers' place in the play-off semi-final on the back of the three straight wins, with three clean sheets a bonus.
Harriers were unable to seriously threaten the home goal but they should have snatched an unlikely lead in the 33rd minute when a cross-cum-shot from Adam Chambers was somehow missed by striker Mark Rawle as he slid in at the back post.
Kirk should have put the home side ahead of the first minute when he latched on to a weak back header by Wayne Hatswell, but despite missing that and two other presentable chances, he eventually came up trumps.