The Central Bureau of Investigation (CBI) had filed an application before the court seeking permission to question Waze, currently in the custody of the National Investigation Agency, earlier in the day.
Judge P R Sitre heard the CBI's plea while extending the NIA custody of Waze till April 9.
Waze was arrested on March 13 in the case of an explosives-laden SUV found near industrialist Mukesh Ambani's house in south Mumbai on February 25 and the subsequent death of Thane-based businessman Mansukh Hiran.
Both these cases are probed by the NIA. Following the order of the Bombay High Court, the CBI late Tuesday night registered a PE to probe allegations of corruption levelled by Param Bir Singh against Deshmukh.
Singh was removed from the post of Mumbai police commissioner and shifted to the Home Guards department on March 17.
He later filed a petition in the HC seeking a CBI probe against Deshmukh, alleging that the NCP leader had asked Waze and other police officers to extort Rs 100 crore from restaurants and bars when he was home minister of the state.
Singh had also alleged corruption in police transfers and postings.
Deshmukh had denied the allegations.
The high court in its order on Monday said the CBI shall carry out an inquiry into the allegations within 15 days and then decide on a further course of action.
After the HC order, Deshmukh resigned as the state's home minister.
Both Deshmukh and the Maharashtra government have approached the Supreme Court challenging the HC''s order.