The date of the allegation dates back to 2005 and took place in the London borough of Lambeth, the location of the Old Vic theater where Spacey was artistic director.
It's unclear if Scotland Yard's investigation relates to one of these complaints.
A Met Police spokesman said: "On Wednesday, November 1, City of London Police referred an allegation of sexual assault to the Metropolitan Police Service".
Scotland Yard confirmed that the allegations were made by a man in Lambeth, home to the theater. However, they did not name Spacey or the victim.
The alleged victim came forward on Friday, more than two weeks after another male said he was assaulted by the same man in 2008.
It's the second investigation regarding the actor after an alleged assault in 2008.
The second allegation was made on Friday, police said.
Spacey has been removed from from the movie "All the Money in the World" and has been dropped from the hit TV series "House of Cards".
The first allegation against Spacey was made by actor Anthony Rapp, who accused him of sexual assault.
Abuse claims against Spacey prompted The Old Vic theatre to launch an investigation into the actor's term as artistic director, between 2004 and 2015, receiving 20 claims of inappropriate behaviour.