Naidoo (61) succumbed to cancer after a long battle.
He was the provincial commissioner for nine years since 2001 until he was replaced by Mzwandile Petros in 2010.
He served the police service for 35 years.
Naidoo was born in Umzinto, KwaZulu-Natal.
Gauteng Premier Nomvula Mokonyane had sent her condolences to the family of the former top cop.
“We are deeply saddened by his untimely death. I know the late commissioner from working together with him during my tenure as an MEC for Safety and Liaison between 1999 and 2004.
“On behalf of the provincial government and the people of this province, we wish to convey our heartfelt condolences to the family and friends of commissioner Naidoo.
“May his soul rest in peace. We wish the Naidoo family strength during this difficult time. Our thoughts are with them,” said Mokonyane.
Details of his funeral were still unavailable.