The Scottish tennis ace hit out after the Leave campaigner shared footage following his flight to Serbia to visit Djokovic's brother to show his support for the world No.1 over a visa cancellation.
Djokovic had been detained from Thursday morning at an immigration facility in Melbourne after his visa was cancelled following scrutiny of the medical exemption he had secured to enter the country.
But the Serbian said he was “pleased and grateful” on Monday after his appeal against the decision to refuse him a visa in the Federal Circuit Court of Australia was successful ahead of the start of the Australian Open.
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The former Ukip leader and now GB News presenter has been vocal in his support for Djokovic over his row with the Australian Government.
Farage had travelled to Belgrade and was spending time with the Djokovic family, sharing clips from Djokovic’s trophy room and opinions on the case on social media.
But three-time Grand Slam winner Murray took aim at Farage over the former politician’s stance considering his continued calls for tougher borders in the UK for many years.
Quoting a tweet from Farage showing footage from the trophy room, Murray posted: "Please record the awkward moment when you tell them you’ve spent most of your career campaigning to have people from Eastern Europe deported."
Former British number one Murray had expressed concern for the Serbian, saying earlier this week his predicament was “really not good for tennis at all”.
The five-time Australian Open finalist said: “I think everyone is shocked by it, to be honest.
“I’m going to say two things on it just now. The first thing is that I hope that Novak is OK. I know him well and I’ve always had a good relationship with him and I hope that he’s OK.
“The second thing, it’s really not good for tennis at all, and I don’t think it’s good for anyone involved. I think it’s really bad.”
Earlier on Monday, Judge Anthony Kelly quashed Djokovic’s visa cancellation and ordered the Australian Government to pay legal costs and release the world No.1 from detention.
Djokovic tweeted: “I’m pleased and grateful that the Judge overturned my visa cancellation. Despite all that has happened, I want to stay and try to compete @AustralianOpen.
“I remain focused on that. I flew here to play at one of the most important events we have in front of the amazing fans.
“For now I cannot say more but THANK YOU all for standing with me through all this and encouraging me to stay strong.”
At a press conference staged by the Djokovic family in Belgrade, his mother Dijana described her son’s successful appeal as “the biggest win of his career – bigger than any of the grand slams he has won”.
She said: “He has done nothing wrong. He hasn’t broken any of their laws, but he was subjected to torture, to harassment.
“He fought against that system and against that government because he thought he had the right to be there with the visa that he got, and he went there to win that tournament.”