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Rublev galloped to an early lead and barely gave his opponent a chance as he closed out the match with a powerful forehand winner for his first win over Djokovic and 11th career title.
The Serb had been automatically listed in the draw for the tournament but said he knew it was unlikely that he would be able to gain entry into the United States.
Djokovic said he was ready to sacrifice his shot at the Grand Slam record over the "freedom of choice" but he was keeping an open mind about taking the jab in the future.
Djokovic was back in training hours after winning that court challenge, thanking the judge who released him from immigration detention and saying he remained focused on trying to win a record 21st tennis major at next week's Australian Open.
The world No. 1 was released from Australian immigration detention on Monday.
Australian Home Affairs Minister Karen Andrews hit back at suggestions by Serbian supporters, including Djokovic's family, that he was being "held captive", stressing the star player is free to leave the country at any time.
Djokovic, who has won nine Australian Open titles including the last three, is holed up in a quarantine hotel in Melbourne as his lawyers sought an urgent injunction against deportation.
Australia's Border Force confirmed Djokovic's visa had been revoked, while the source said the player's lawyers planned to file an injunction to prevent his removal.
The artwork was done by Boban Savic, with references to some of Djokovic's greatest accomplishments, including his 37 ATP Masters 1000 titles and 20 major triumphs.
Nikola Mektic and Mate Pavic beat Novak Djokovic and Filip Krajinovic 7-5, 6-1 in a decisive doubles clash.