Tom opened the scoring on 53 minutes through Tomi Pugin and four minutes later had the chance to double their lead from the spot, but Mikhail Kerzhakov saved the penalty.
On 72 minutes, Danil Lesovoy scored a beautiful goal from outside the box and on 86 Ilya Zuev scored the winner to the delight of the Zenit-2 fans.
Having defeated Tom, the blue-white-sky blues second team moved to 17th place and will face Khimki at home on 2 May.
