"I do not want to proceed with this matter when you are in this state of mind," Kgomo told the court as defence counsel Laurence Hodes SC continued his cross-examination of Nassif.
This was Nassif's fourth day on the witness stand and it had been turbulent.
Nassif's voice cracked as he continued to answer questions on Tuesday afternoon.
"We've done enough for the day," said Kgomo.
"Take my advice (to rest), I'm not forcing you," Kgomo told Nassif.
He was testifying at Agliotti's trial on four charges, two of conspiracy to commit murder, one of attempted murder and another of murder.
Nassif is a section 204 witness, which allows for indemnity from prosecution provided his testimony to the court was truthful.
The trial continues on Wednesday.