The majority of the 15,000 crowd went home happy after two first-half goals handed Portsmouth all three points amid signs of a revival on the South Coast after a wretched few years.
Northampton's night was compounded by confirmation from manager Chris Wilder that midfielder Ian Morris is out for the season with a knee injury suffered in training on Monday.
That blow, together with the absence of Darren Carter from the Cobblers engine room means Wilder is set to enter the transfer market sooner rather than later and look for a loan signing.
His side return to Sixfields on Saturday afternoon when Shrewsbury are the visitors.