Issa Alekasir scored twice in the 80th and 88th minutes in Tehran’s Takhti Stadium.
Tractor Sazi coach Yahya Golmohammadi had been given one last chance to salvage his career in the Tabriz-based team.
Tractor Sazi general manager Mustafa Ajorloo had already said if the team loses to Naft Tehran, they will hire former Pas and Persepolis coach Mustafa Denizli.
Also on Thursday, Esteghlal Khuzestan edged past Padideh, thanks to a goal from Vahid Namdari in the 42nd minute.
Paykan and Sepidrood Rasht also played out a goalless draw.