The game took place at the Gazprom Arena stadium and ended in a 2-0 victory for the hosts.
Zenit striker Mateo Cassierra opened the scoring in the 23rd minute, and doubled the lead in the 34th minute.
The next rival of St. Petersburg in the Cup of Russia will be the Samara "Wings of the Soviets".
"Fakel" will meet with the Moscow "Spartak".
Both games will be played on September 14th.
The start is at 19:00 Moscow time.
Earlier it was reported that CSKA Moscow beat Torpedo away in the first round match of the Russian Cup group stage.