"This is not an appeal against the decision of the executive government," Allsop told the court.
"It is an application to the court as a separate arm of government being the Commonwealth judicial branch to review a decision by a member of executive, the minister, for the lawfulness or legality of the decision on the three grounds put forward.
"These grounds focus on whether decision was for different reasons irrational or legally unreasonable. It is no part or function of the court to decide upon the merit or wisdom of the decision."
Djokovic was automatically banned from Australia for three years following the decision but may be allowed back in if the government believes there are exceptional circumstances.
The court's full reasons for deporting Djokovic were not published on Sunday — they will instead be published on Thursday afternoon.
The Serbian star made a statement after the decision by the Federal Court on Sunday.
"I'd like to make a brief statement to address the outcomes of today's Court hearing," he said. "I will now be taking some time to rest and to recuperate, before making any further comments beyond this.
"I am extremely disappointed with the ruling to dismiss my application for judicial review of the decision to cancel my visa, which means I cannot stay in Australia and participate in the Australian Open. I respect the Court's ruling and I'll co-operate with the relevant authorities in relation to my departure from Aus.
"I am uncomfortable that the focus of the past weeks has been on me and I hope that we can all now focus on the game and tournament I love. I would like to wish the players, tournament officials, staff, volunteers and fans all the best for the tournament.
"Finally, I would like to thank my family, friends, team, supporters, fans and my fellow Serbians for your continued support. You have all been a great source of strength to me."
On Tuesday evening, two days into the tournament, Tennis Australia finally addressed the situation.
In a statement, the TA board said it "deeply regrets" the events that led the world's best male tennis player to travel to Australia under the impression he had a medical exemption that meant he did not need to be vaccinated against Covid-19.
"The board and Member Associations commend the Tennis Australia CEO (Tiley) and the entire Tennis Australia team for their hard work and dedication to delivering a spectacular summer of tennis," the statement read.