Domagoj Drozdek netted a brace for the hosts in the 47th and 51st minutes but Hadi Habibinejad pulled a goal back from the penalty spot in the 57th minute.
Tomislav Strkalj made the scoreboard 3-1 from the penalty spot in the stoppage time,Tehran Times said.
Tractor moved up to third place with 16 points, two points adrift of leaders Persepolis with one game at hands.
Elsewhere, Aluminum and Fajr Sepasi shared the spoils in a 1-1 draw in Arak.
On Sunday, Esteghlal will host Foold and Sepahan play Mes in Rafsanjan.
IRNA