The New York Times newspaper had alleged Spitzer was the man identified as "Client 9" in a federal affidavit regarding an investigation into a prostitution service.
Spitzer will be replaced on Monday by Lieutenant Governor David Paterson, who will be the city's first African-American governor.
'Tough stance'
The affidavit said that "Client 9" arranged to meet "Kristen" - a prostitute who charged $1,000 an hour - on February 13 in a Washington hotel and then paid her $4,300, the court document said.
The complaint relates to four people being charged last week with running a prostitution network called The Emperor's Club.
It is not known if Spitzer will face any charges relating to the case.
Spitzer became well known for his tough stance towards Wall Street on financial crime while the state's attorney general, and entered the governor's office in November 2006 on a pledge to clean up the state's political machine.