Auburn police said they arrested the rapper after a woman called emergency services at 03:48 to report an assault.
Nelly strongly denies the allegations and has now been released.
The artist tweeted: “I have not been charged… therefore no bail was required.
“I was released, pending further investigation.”
Nelly, whose real name is Cornell Iral Haynes Jr., tweeted that he was “beyond shocked that I have been targeted with this false allegation”.
“I am completely innocent,” the artist said.
“I am confident that once the facts are looked at, it will be very clear that I am the victim of a false allegation.”
According to TMZ, Nelly was taken into custody on a second degree rape charge.
In a statement, the artist’s lawyer also described the allegation as “completely fabricated”.
Scott Rosenblum said in a statement: “Our initial investigation clearly establishes this allegation is devoid of credibility and is motivated by greed and vindictiveness.”
Nelly, 42, is best known for his No 1 hits Hot in herre and Dilemma, but has not released new music for a number of years.
In 2015, the rapper was arrested on felony charges after police found drugs and guns on board his tour bus.
He is currently on tour with the Backstreet Boys and Florida Georgia Line, and performed in Auburn on October 6.
The bus was parked near a local Walmart at the time of the alleged incident. A police statement said they were continuing to investigate.
Nelly was due to perform on the Smooth Stadium Tour in Ridgefield near Portland on October 7.
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