Judge Anthony Kelly has earlier ordered the release of the tennis star from detention.
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Djokovic has been detained since early Thursday at an immigration facility in Melbourne after his visa was cancelled.
The decision comes just days before the Australian Open is set to begin in Melbourne.
All participants at the Australian Open, which starts on January 17, need to be vaccinated against COVID-19 or have a medical exemption, assessed by an independent panel of experts.
The 41-year-old turned out at three Grand Slam tournaments in 2021 but dealt with multiple injury problems throughout the calendar year.
The world number one, who has won at Melbourne Park on nine occasions, has repeatedly refused to say whether he has been vaccinated against coronavirus having previously expressed hesitancy over being jabbed.
Serbia’s Djokovic, 34, has not spoken publicly about his vaccination status.
“I am experiencing some unpleasant moments but I hope that I will improve little by little,” Nadal wrote on Twitter. “I am now confined at home and have informed those people who have been in contact with me of the result.”
The 34-year-old Djokovic, who would be bidding for a record-breaking 21st Grand Slam title in Melbourne, has refused to say whether or not he has been vaccinated against coronavirus.
The 40-year-old has not taken to the court since this year’s Wimbledon, during which he bowed out at the quarter-final stage to Hubert Hurkacz.
The 40-year-old picked up the problem during the first round of Wimbledon against Belarus’ Aliaksandra Sasnovich and was forced to pull out of the competition.
The Japanese player has been fined £12,900 (€15,000) after deciding to boycott press conferences at the tournament. Osaka announced on Wednesday that she would not be conducting press conferences at the tournament, which began on Sunday and runs until May 13.
Nadal trailed 4-2 in the opener but recovered, breaking twice to take it.
Federer, 39, is making his comeback after two knee operations and has not played a Grand Slam since January 2020.
Djokovic produced a clinical 6-4 6-2 win over up-and-coming Jannik Sinner on Wednesday before Nadal, the 11-time champion at the Country Club, thrashed Federico Delbonis 6-1 6-2.
Federer, who has needed two operations to correct a long-standing knee issue, is due to play in the Qatar Open this week.
His latest triumph in Melbourne has brought the 33-year-old world number one Djokovic to within two of the record mark of 20 major wins shared by Roger Federer and Rafael Nadal.
The 23-year-old defeated first-time slam finalist Jennifer Brady of America 6-4 6-3 to regain the title she won in 2019.
The world number one, who has won the title on each of the eight previous occasions he has reached the semi-finals in Melbourne, claimed his first straight-sets win since the first round, beating the world number 114 6-3 6-4 6-2.
The mother of one could barely respond before her voice broke and she began crying, leaving the room and ending her press conference.