Team Melli stole a crucial three points away from home despite the White Wolves dominating the chances and having a Odil Akhmedov goal controversially not allowed
Team Melli, who haven't reached a World Cup finals since 2006, took a huge step forward in their campaign to qualify for Brazil 2014 as one of the top two teams of Group A, as they beat one of their toughest competitors Uzbekistan.
Carlos Queiroz's side started with the unusual defensive formation of Hossein Mahini, Sayed Jalal Hosseini and Pejman Montazeri at the back and created very few chances throughout the match in a game which seemed destined for a goalless stalemate before Khalatbari's dramatic 94th-minute strike.
However, Uzbekistan will feel a sense of injustice after Odil Akhmedov's close-range effort in the 72nd minute appeared to cross the line only for referee Yuichi Nishimura to not allow the goal to count.
Earlier, Victor Karpenko had the opening chance to score on 21 minutes, only to be denied by Iran goalkeeper Mehdi Rahmati, who had a busy afternoon keeping his opponents at bay on numerous occasions.
The Esteghlal keeper made another sharp save barely six minutes later from Geynrikh, while the same player had the ball in the back of the net on 41 minutes, however it was disallowed for offside.
Uzbekistan continued to dominate the game in the early stages of the second 45, with Iran offering very little in an attacking sense.
The hosts should have taken the lead on 72 minutes when Geynrikh whipped in a free-kick which created a goalmouth scramble, with the ball hitting the post and rebounding to Akhmedov. The Anzhi Makhachkala man appeared to poke the loose ball over the line before Sayed Jalal Hosseini's block but the assistant referee and Nishimura waved play on despite the Uzbek protests.
On 85 minutes, Rahmati looked to have confirmed himself as man-of-the-match with another stellar save to deny Timur Kapadze's long-range drive before Khalatbari's late winner.
The strike came three minutes into stoppage-time and out of nothing as substitute Karim Ansarifard produced a fine ball for Khalatbari which evaded the Uzbekistan defence, leaving Al Wasl man Khalatbari to slide past Uzbekistan keeper Ignatiy Nesterov and leave the hosts devastated.