The former Watford player scored eight minutes from time to cancel out Simon Whaley's opener for the Shakers, but it was a point that the Cobblers scarcely deserved as they lost their way trying to break down their 10-man opponents.
Bury had striker Allan Smart sent off after 64 minutes. He had already been booked in the first half by referee Darren Deadman for a foul when some ill-considered backchat saw him given his marching orders.
Bury were also hampered by having to change their goalkeeper early in the second half. Neil Edwards, who let in five here last season for Rochdale, made a great save from Bradley Johnson just before the break but was injured in the process which enabled Craig Dootson to take his place after 49 minutes.
Whaley, who had almost given the visitors the lead with a sixth minute curling shot which was pushed away by Lee Harper, beat the goalkeeper with a cool finish in the 26th minute.
He was a revelation in trying to ease the pressure on the overworked Bury defence, but Northampton became increasingly frustrated in their efforts to break through.
This was summed up in the 62nd minute when an inch-perfect cross from Josh Low should have been headed into the net by either Jason Crowe or Ian Taylor. In the event, they tangled with one another and Bury escaped.
The equaliser, hooked in by Gilligan after Taylor headed back a cross from David Galbraith, prompted the inevitable late rush from the home side and a screamer from Crowe flashed wide before Taylor headed a Galbraith corner wide of the target.
Had either of those gone in it would have been tough on Graham Barrow's men.