Jones, 23, appeared in Jefferson District Court before Judge Sheila Collins immediately after turning himself in to authorities. He was released to home incarceration. He did not speak during the brief hearing.
According to the warrants issued, Jones was charged with assaulting two women early Sunday, both of whom were able to identify Jones as the alleged assailant. One of the women was identified as a University of Louisville student.
His attorney, Scott Cox, said Jones is cooperating with the police investigation.
"We believe this gentleman is innocent and he's been falsely accused, and he's going to be found not guilty," he said. "We understand there's video potentially in the hallway of the building where this allegedly occurred, also video out in the parking lot. We believe those videos will be exculpatory to Mr. Jones."
Jones has withdrawn from classes at the university and has moved out of the athletic dorm and into a hotel room, Cox said.
"I'm totally saddened to the point of disbelief," Louisville coach Rick Pitino told reporters Thursday. "... We've built a very strong culture here of discipline and doing the right things ... There's not one time been any of this type of misconduct in his past, so it comes as a shock. He's the type of guy that in practice, if he does the wrong things, he could get in a fight very easily, but nothing that any of us would ever believe this could happen."
Pitino said Jones sent him a text after he was dismissed from the team which read: "Thank you for everything you've tried to do for me. I'm sorry for what I've done to the team go out and tell the team to win a championship."
Jones had been suspended by Pitino on Feb. 17 before the team's game at Syracuse. At that time, Jones was cited in a report by university police for sending a threatening text to a former girlfriend.
That woman, who decided against prosecuting Jones, is not one of Jones' alleged rape victims, according to the Louisville Courier-Journal.
Jones was reinstated after he and the former girlfriend both met with the university's dean of discipline, sources told ESPN.com on Thursday. The university hearing, which also took into consideration that Jones' former girlfriend had broken electronics in his room, determined that no crime was committed and told both individuals to stay 500 feet from each other and have no further contact.
Jones then played in the Cardinals' win over Miami on Saturday afternoon, before the alleged sexual assaults.
On Sunday, the university announced without further explanation that Jones had been dismissed from the team.
In a statement, the school said: "(Jones) was permitted to return to the team on Feb. 19 with strict internal disciplinary measures attached, among which included a curfew. It was discovered shortly after noon on Feb. 22 that Chris had violated a curfew and there were other accusations, without knowing specifics. At that time, Chris was immediately dismissed from the team."
Two others are charged in the alleged attack on the second woman. Jalen D. Tilford is charged with rape and sodomy, and Tyvon Julah Walker is charged with rape. They were arrested, and the judge set a bond of $75,000 for Tilford and $100,000 for Walker.
Jones, a senior from Memphis, started in 24 of the 26 games he appeared in this season. He averaged 13.7 points, 4.0 rebounds and 3.6 assists.
Information from ESPN.com's C.L. Brown, Dana O'Neil and Andy Katz and The Associated Press was used in this report.
Jones Pleads Not Guilty To Rape Charges
Lt. Col. Kenneth Brown, the University of Louisville's assistant chief of police, discusses the investigation into former Louisville guard Chris Jones' alleged sexual assault of two women.
Pitino: We're All Shocked, Saddened
Louisville coach Rick Pitino talks about former guard Chris Jones being charged with rape and sodomy and how Jones acted after being dismissed from the team.
Ex-Louisville Guard Faces Rape Charge
ESPN college basketball Insider Jeff Goodman discusses the sexual assault allegations against former Louisville guard Chris Jones, who was kicked off the team by coach Rick Pitino.