All of the main action at the Ricoh Arena came in the opening 18 minutes of the game as Zander Diamond and Marc Richards scored for the Cobblers, Jacob Murphy equalising in between for League One highfliers City.
Town always posed a threat going forward and defended solidly to take their place in the next round of the famous old competition, off-field issues not withstanding.
Manager Chris Wilder clearly had those issues in mind when speaking to the official NTFC website after the game.
He said: "It's a day to remember in the history of this proud football club, this club has over a hundred years of history and surely we can get things resolved.
"The club is the most important thing in all of this and it must continue."