Lord Macfadyen gave ministers 72 hours to transfer Mr Napier from Barlinnie prison in Glasgow to accommodation which complied with human rights legislation.
Robert Napier went to court arguing that his detention in a cell without integral sanitation was against his human rights.
Lord Macfadyen ruled on Tuesday at the Court of Session that slopping out was "inhumane and degrading" and that Mr Napier should be transferred.
Mr Napier has now been moved pending a full legal appeal of the judge's decision by the Scottish Executive.
Lord Macfadyen gave ministers 72 hours to transfer Mr Napier from Barlinnie prison in Glasgow to accommodation which complied with human rights legislation.
The judge said that slopping out - whereby prisoners use a pot or bucket as a toilet in their cells - was "inhumane and degrading".
The Scottish Executive feared that, following the ruling, hundreds of prisoners would seek to be moved, causing a massive headache for the overstretched Scottish Prison Service.
Executive lawyers lodged an appeal, which was due to be heard on Friday.
Shortly before the hearing was due to start, it emerged that an agreement had been reached between Mr Napier's legal team and the executive for him to be moved to different accommodation in the prison, pending a full legal debate on the issues involved.
Prisons upgrade
Jonathon Mitchell QC, representing Mr Napier, said that the full hearing was likely to go ahead in September.
He added: "There is an awareness on both sides that this is a case that does raise issues of substantial importance and if we go off half-cocked they will never get properly determined."
Justice Minister Jim Wallace has said the executive is committed to ending the practice of slopping out in Scottish prisons.
But he declined to give a deadline for when the practice will cease.
Mr Wallace pointed out that at the beginning of the 1990s only 40% of cells had night toilet facilities - a figure which has now increased to 76%.
He said upgrading work at several facilities would improve the situation further.
And he added that he was awaiting a prison estates review and only after
there has been consultation and debate following that report could he give an
exact indication of when the practice will end.
However, it is likely to be within five years, he said.
A Scottish Prison Service spokeswoman said slopping out was being phased out at the five jails where it is still practised - Barlinnie, Edinburgh, Perth, Peterhead and Polmont young offenders' institution - over the next four years.
Mr Napier has been in prison since 18 May, when he was arrested after failing to appear at the High Court in Glasgow to answer charges of assault, robbery and abduction.
His legal action sought transfer from Barlinnie and compensation of £5,000.
Other prisoners are understood to have met solicitors with a view to taking similar action.
Prison officers also warned that they could take action because they have been forced to deal with slopping out.