Another upset looked on as Liam Davis gave the visitors a shock lead at Portman Road but Championship side Ipswich fought back quickly to lead at the interval.
Roy Keane's men were pushed all the way however and only wrapped up the game late on when Tamas Priskin struck.
So a cup run that saw Northampton pull off one of the greatest ever results in the club's history is over and thoughts turn straight away to the battle to move away from the foot of League Two.
"We've got bigger fish to fry now," admitted boss Ian Sampson afterwards.
"If they keep believing in each other we will be OK and I am confident that we can get out of the predicament we are in the league.
"It has been a great cup run. The win at Liverpool will live long in the memory for everyone connected with the club. But livelihoods depend on results at this club now and it is time to put that right."