The performer, 52, was arrested on Wednesday over the unpaid support for three children he has with Andrea Lee. The Cook County Sheriff's Office had said he would have to pay the full amount to be freed.
Sam Randall, a spokesman for the sheriff's office, said in a phone interview on Saturday that the source of the payment was unclear, noting that the name section of the bond slip was left blank.
"Anonymity in this situation is pretty rare," Mr Randall said. "Typically that section of the form is filled out."
Celebrity website TMZ, which cited sources close to Kelly as saying an unidentified benefactor helped him, reported that he was met by screaming fans as he left the jail.
"I promise we're gonna straighten all this out," TMZ quoted Kelly as telling the group as he walked away. "That's all I can say right now. I love my fans."
Last month, Kelly was arrested and pleaded not guilty to charges he had sexually assaulted three teenage girls and a fourth woman. He has denied similar abuse allegations for decades. In 2008, the singer was tried on child pornography charges and found not guilty.
Kelly bailed out of jail on the sexual assault charges on February 25 and had since complained of financial difficulties, saying in an interview with CBS that "so many people" had access to his bank account and had stolen from him.
In the interview, he also tearfully and angrily rejected allegations that he had sex with underage girls.