Ronnie Coulter, 48, from Wishaw, denies murdering Mr Chhokar, 32, in Overtown, North Lanarkshire, on 4 November 1998.
He has lodged a special defence blaming his nephew Andrew Coulter, and another man, David Montgomery.
Judge Lord Matthews told jurors: "In order to convict Ronnie Coulter you must be convinced he used a knife and stabbed the deceased."
At the High Court in Glasgow, the judge told the 10 women and four men to take as much time as they needed.
Lord Matthews said: "It's not a case where you want to rush to judgement and I'm sure you won't do that."
The judge also told the jurors there were three verdicts open to them - guilty, not guilty or not proven.
The jury has already heard that Ronnie Coulter, his nephew Andrew and Mr Montgomery went to see Mr Chhokar on the night he died following a row over a Â£100 Giro cheque.
After an altercation, Mr Chhokar collapsed in front of his partner Liz Bryce.
He was stabbed three times in the chest and one of the blows pierced his heart, resulting in his death from massive blood loss.
The court has also heard how Ronnie Coulter was previously tried for Mr Chhokar's murder in 1999, but cleared of the charge.
Andrew Coulter, who was convicted of stabbing and killing another man in 1999, and Mr Montgomery, were also cleared of Mr Chhokar's murder at another trial in 2000.
Both men have given evidence during the most recent trial and admitted being there on the night Mr Chhokar died, but they denied murder.
The jury in the Surjit Singh Chhokar murder trial has been sent out to consider its verdict.