Sibiya was set to face a disciplinary hearing on Monday but his lawyers tendered his letter of resignation at the start of the proceeding, police spokeswoman Athlenda Mathe said.
"As the former senior officer had an ongoing disciplinary case against him at the time of his resignation, his departure from the service is therefore regarded as a dishonourable discharge," Mathe said.
Sibiya is currently in prison after he was arrested for alleged rape and grooming of a minor last month.
He has denied the charges.
His application to be released on bail has been postponed to October 13.
Sibiya has been the subject of a judicial commission of inquiry investigating wide-ranging allegations of corruption within the South African police and alleged ties to the country's criminal networks.
At the commission, which is chaired by retired judge Mbuyiseni Madlanga, Sibiya has been accused of receiving large sums of cash and gifts from alleged criminals.
During his testimony at the commission, Sibiya denied all allegations against him.
He had been suspended since September last year.
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