Team Melli won 1-0 at Suncorp Stadium in Brisbane courtesy of an injury-time header from Reza Ghoochannejhad - which Ali also claimed should have been ruled out for offside.
The Emirates now appear bound for a quarter-final against Japan, and will have to face the Asian Cup holder without key defender Walid Abbas, who was shown his second yellow card for the tournament and is now suspended for the next match.
Sato cautioned Abbas for his 26th-minute challenge on Iran's Alireza Jahanbakhsh.
Ali said it was "not even a foul" and suggested the decision to appoint Sato as the referee was part of a plot to help Japan avoid an early meeting with Iran and damage UAE's chances of going deep into the tournament.
"I'm just surprised how the game was given to a Japanese referee and maybe we play against Japan," he said in his post-match press conference.
"He give a yellow card immediately to the player who will be suspended for the next game. That's very strange."
Ali also said Sato was effectively conned into awarding Ghoochannejhad's goal because the Iran players were "very clever" and ran away to celebrate before he could pull them back.
Replays, however, confirmed all players were onside when Adranik Teymourian's hopeful half-volley was sent into the box in the first minute of added time.
Ali refused to comment on Australian referee Ben Williams, who controlled the Group B match between Saudi Arabia and Uzbekistan on Sunday, but his veiled response indicated where his sentiments lie.
Uzbekistan was at one stage a potential quarter-final opponent for the Socceroos and Williams showed seven yellow cards in the 3-1 win to the White Wolves.
"I think this question has to be transferred to the AFC to comment on this, because I cannot comment on this," Ali said.
Ali's counterpart, Iran coach Carlos Queiroz, was fined $3000 earlier for criticising Williams.
The wily Portuguese manager wasn't about to make the same mistake twice.
"You must think I am a guy from charity," he said when asked for his response to Ali's comments.
"I don't want to make more donations."
