British-born Shia cleric Sheikh Farrokh Sekaleshfar lectured near Orlando, Florida in April and was being widely quoted in the wake of Sunday's killing.
He was visiting Australia as a guest of Sydney's Imam Husain Islamic Centre.
Media reports on Wednesday said Sheikh Sekaleshfar left the country after Prime Minister Malcolm Turnbull ordered a review of his visa.
Australia's immigration minister Peter Dutton said he had officially revoked Sheikh Sekaleshfar's visa and that it would be "very difficult, if not impossible for him to return" to the country.
But Mr Dutton defended his department against accusations that a visa for the sheik should never have been approved.
'It's difficult for the department to go through the Facebook or social media postings of millions of millions of people each year who seek visas,' Mr Dutton told Sky News.
Sheikh Sekaleshfar was born in Manchester, UK and currently lives in Iran.
In April he delivered a sermon entitled How to Deal with the Phenomenon of Homosexuality at the Husseini Islamic Center in Sanford, Florida.
There is no evidence that Omar Mateen, who killed 49 people at an Orlando nightclub, attended the lecture.
During lectures, clips of which were posted online, the cleric has said the death penalty is justified for homosexuals in societies operating under Islamic laws.
"Death is the sentence. There's nothing to be embarrassed about this. Death is the sentence," he said during a 2013 lecture at the University of Michigan.
He told Australia's Daily Telegraph newspaper that his comments had been taken out of context and said he did not believe his words could have inspired Mateen's nightclub attack.
Sheikh Sekaleshfar said Mateen was a follower of the so-called Islamic State, which follows the Wahabi doctrine of Sunni Islam and had been "killing homosexuals in the most wrongful way for years now", whereas he was a Shia scholar.
"This barbaric act was beyond all definitions of humanity," he told the paper.
An Islamic preacher who has said homosexuals should be put to death has left Australia.