Ganguly hit a boundary in his short innings before being caught behind off an Azhar Mahmood delivery as Northants ended the day with Usman Afzaal (28) and Charl Pietersen (2) holding fort.
Earlier, the former Team India captain took the wicket of Rikkie Clarke (47) after Surrey decided to bat first and piled up 328 all out in their first innings of the four-day match.
Ganguly's figures read 11-2-36-1.
Ali Brown made 113 for Surrey and decent contributions by Mark Ramprakash (51) and Rikki Clarke (47) helped the visitors put up a fighting total on board.
Matt Nicholson took four wickets for 84 for Northants.
In another Division two County Championship match Dinesh Mongia failed to open his account as Leicestershire made 354 for six on the first day of their match against Glamorgan at Sophia Gardens.
Mongia was dismissed after facing seven deliveries by Dean Cosker, who got him caught behind by wicketkeeper Mark Wallace.
Hylton Deon Ackerman was unbeaten at 177 after the visitors opted to bat first after winning the toss.
Ackerman and Paul Nixon (60) put on 160 for the sixth wicket as the visitors posted a record total against the Welsh county.