Judges rejected a challenge launched by the unvaccinated tennis star after the government canceled his visa on “health and good order” grounds.
The world number one’s hopes of defending his Australian Open title and winning a record 21 Grand Slams in Melbourne are over.
“I respect the Court’s ruling and I will cooperate with the relevant authorities in relation to my departure from the country,” he said in a statement, wishing the tournament well.
He boarded an Emirates flight bound for Dubai.
The player’s family said they were “very disappointed” by the decision and the fact Djokovic had to leave Australia.
“Despite the scandalous behavior towards Novak, we believed that the sport would win,” they said in a statement.
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As he prepared to leave, the ATP, the men’s tennis governing body, said the court’s decision on Sunday marked the end of a “deeply regrettable series of events”.
Earlier in the day, Djokovic’s supporters stood silently outside the courthouse as the decision was announced on the eve of his opening match at the tournament. One fan told the BBC her summer would be “empty” without the 34-year-old playing in the Open.
Australian Prime Minister Scott Morrison hailed “the decision to keep our borders strong and keep Australians safe”.
Djokovic opened the case after Immigration Minister Alex Hawke used his ministerial powers to cancel the Serbian player’s visa, arguing that his presence in the country risked heightening anti-vaccine sentiment.
It was the second time his visa had been revoked, after a first cancellation for not following Covid entry rules was overturned by a different judge.
During Sunday’s hearing before a panel of three judges, Djokovic’s defense unsuccessfully argued that the pleas given by the government were “invalid and illogical”.
Court president James Allsop said the federal court’s decision was based on the legality of the minister’s decision, not whether it was the right decision to make.
The full rationale for the decision will be released in the coming days, he said.
Deportation orders usually include a three-year ban on returning to Australia, although this may be waived in certain circumstances.
Sunday’s decision marks the end of a 10-day saga over Djokovic’s Australian visa.
The federal government has repeatedly said that people must abide by the strict laws in place to deal with the pandemic and that no one is “above the law”.
Djokovic was originally granted a medical exemption to enter Australia by two different independent health panels – one commissioned by Tennis Australia and the other by the Victorian state government – after testing positive for coronavirus in mid-December.
However, the Australian Border Force detained him on January 5 for failing to meet federal coronavirus requirements and his visa was revoked.
A judge later overturned that decision, but the government stepped in last Friday to revoke the visa again, saying it was in the public interest.
Although Djokovic is not vaccinated against Covid-19, he has not actively promoted anti-vaccine misinformation.
The visa battle is also at the heart of a political dispute in the country.
But Australian opposition politician Kristina Keneally said Morrison had become a laughingstock for mishandling the Djokovic case, questioning why the unvaccinated player received a visa in the first place.
Morrison and his government also faced the anger of Serbian President Aleksandar Vucic.
“He [Djokovic] came to Australia with a proposal for a medical exemption and then you mistreated him for 10 days. Why did you do that? Do a witch hunt against him? This is something no one can understand,” he said.
British tennis player Andy Murray, who has known Djokovic since he was a child and competed against him for the sport’s biggest prizes, said the situation was “not good” for anyone.
“It seems like everything here happened extremely at the last minute and that’s why it became such a mess,” he told the BBC.
Djokovic said on Sunday that he was “uncomfortable” with the focus placed on him as a result of the visa dispute, adding: “I hope now we can all focus on the game and the tournament I love.”
Italian Salvatore Caruso, ranked 150th in the world, is the “lucky loser” who will now replace Djokovic in his match against Serbian Miomir Kecmanovic on Monday.