Ganguly didn't get the chance to bat in the first innings as Northamptonshire declared at 269 for three in 62.3 overs with Stephen Peter slamming a 194-ball knock of 142 with the help of 26 boundaries.
Pakistan, in reply, scored 250 for nine in 64.5 overs with Younis Khan topscoring for the visitor with 58.
Ganguly, with his gentle medium pace, got the wicket of Kamran Akmal who was caught by David Sales on 38. Ganguly's figures read 6-1-19-1.
Northamptonshire were reduced to six for two in their second innings when Ganguly stepped in, hoping to overcome his poor run with the bat for the club.
Ganguly, ignored for next month's tri-series in Sri Lanka, was batting on five off 17 balls when Nazir hurled a bouncer and the southpaw went for a hook. The mistimed shot saw him edging the ball onto his chin resulting in a small gash, which eventually required two butterfly stitches and Ganguly didn't come to bat again as his team was skittled out for just 140 to leave the tourists needing 160 for victory.
Pakistan were 24 for no loss in seven overs with opener Salman Butt (15) and Imran Farhat (9) in the crease.