The first goal of the game came in the 71st minute when Terentyev set up Markin after cutting in from out wide and the Zenit-2 forward struck with one touch to make it 1-0.
Six minutes later, Prokhin scored after a corner and Ivanov finished off the surprise win on 79 minutes to make it 3-0. Mordovia pulled one back on 84 mins but the points were secured by then.
Having won the last home game of the season, Zenit-2 climbed to 19th place in the table above next week's rival Tyumen, who they play away on 19 May.