The deposed Team India captain just managed to hit a boundary before being bowled by RL Johnson after facing nine balls but a quickfire 62 off 40 balls by DG Sales helped Northants successfully chase a target 191 set by the visitors.
Put in to bat first, Somerset wrested the initiative with Aussie Test opener Justin Langer hitting a quick-fire 67-ball 97.
Langer shared a 71-run first wicket partnership with MJ Wood before Ganguly struck, dismissing Wood for 43.
The southpaw then had CL White stumped for 10 putting the brakes on Somerset's scoring. The visitors were eventually bowled out for 188 with Monty Panesar chipping in with two wickets as well.
Ganguly's figures read 4-0-20-2.
The Northants' began their reply on a shaky note as Ganguly departed for four but contributions by Sales and other middle-order batsmen, including a 16-ball 28 by Lance Klusener, saw the hosts reaching the target with five wickets and three balls to spare.
Meanwhile, in another Twenty20 Cup match, Dinesh Mongia failed to make much impact, making 20 off 21 balls as his team Leicestershire beat Derbyshire by 18 runs at the Grace Road.