The result saw the capital Reds go top of the table for hours, but Sepahan defeated Havadar 3-1 at home later on Sunday to restore the lead in the Iranian top flight.
Tractor started on the front foot and could have gone in front, had it not been for Iranian international keeper Alireza Beiranvand denying Ricardo Alves and Reza Asadi in one-on-one situations.
Still, Yahya Golmohammadi’s men seemed to be on their way to a commanding victory when Mohammad Omri and Mehdi Torabi combined twice to give the visiting side a two-goal cushion by the half-hour mark.
The introduction of Mohammad Abbaszadeh – whose goal saw Tractor beat Persepolis in the reverse fixture back in October – nine minutes after the break turned the game on its head as the former Reds’ striker cut the deficit to one with a 67th-minute header and then sent Beiranvand the wrong way from the spot with six minutes left on the clock for his eighth goal of the campaign.
Just when Persepolis was headed for a frustrating draw, 22-year-old Khanonov emerged as the unlikely hero, tapping in from close range after a couple of his teammates’ attempt on a Soroush Rafiei’s free-kick had been blocked.
The last-gasp winner means only a single point separates Sepahan and Persepolis before they go head-to-head at Tehran’s Azadi Stadium next Saturday.
In-form midfielder Farshad Ahmadzadeh’s sublime long-range strike gave Sepahan the lead with 10 minutes into the game in Naqsh-e Jahan Stadium and then Shahriyar Moghanlou made it two with a spot-kick three minutes later to join Tractor duo Abbaszadeh and Asadi as the league’s top scorers.
Ramin Rezaeian could have put the game to bed before halftime, only to see his penalty kick kept out by Havadar keeper Mohammadreza Khaledabadi.
Hossein Sadeqi gave Havadar a lifeline two minutes after the interval but Brazilian substitute Ygor Catatau secured maximum points for the host in the 74th minute.
Elsewhere, Paykan and Zob Ahan played to a goalless stalemate in Tehran, while Mes Rafsanjan hammered San’at Naft Abadan 4-0 at home to reduce the gap on fifth-placed Tractor to two points.
Brazilian Jeferson Bahia netted twice inside nine minutes in the first half, before Mehrdad Rezaei put the game beyond visitors’ reach on the hour mark and Qaem Eslamikhah capped off an emphatic display by Mohammad Rabiei’s side from the spot in the stoppage time as San’at remains struggling in the relegation zone.