The former Team India skipper was not much of a success with the ball either as he took just one wicket of Nick Knight (40) conceding 18 runs in two overs.
Warwickshire decided to bat first after winning the toss and set a target of 187 for Nothants. Knight and Tim Ambrose (48) were the top scorers for them.
Chasing the target, Northants got off to a fine start with Usmaan Afzal (21) and Ganguly putting up 44 runs for the opening wicket.
However, Afzaal's dismissal triggered a middle order collapse as Northants lost three wickets in the space of 25 runs.
Ganguly was the next to go with Northants still needing more than 100 runs for victory. His 23-ball innings saw him hit five fours.
Northants could not recover from the collapse and despite a valiant 44 by Riki wessels, the club fell short by 20 runs.