A spokeswoman for the Los Angeles County District Attorney's office said Jones surrendered to authorities at police headquarters Thursday after a warrant for his arrest was issued.
"We charged him with one count of using a minor for sex acts and one count of possession of child pornography," said Jane Robison.
Using a minor for a sex act is a felony. Possession of child pornography is a misdemeanor. Robinson said if Jones is convicted on both counts he faces a maximum prison term of three years.
"If convicted he's going to be a registered sex offender for the rest of his life," said Robison.
Jones was released on $20,000 bail. He is scheduled to be arraigned Thursday in Los Angeles.
Police began investigating Jones in November 2001. The Los Angeles Times reported that investigators were looking into a claim by a 17-year-old boy that the 56-year-old actor used the teen in a sexually oriented film.
The investigation led police to Jones' home, where they said they confiscated evidence of child pornography possession. Robison declined to describe the evidence.
Jones' attorney, Jeff Brodey, told the paper his client has been cooperating with police and prosecutors since the investigation began.
"This is all about photos," said Brodey. "There's not allegations of any touching or any improper acts with a minor."
Brodey said Jones is a "very decent guy" and said the actor's life "shouldn't be ruined" by the case against him.
"This will be resolved very quickly so he can get on with his life and get back to work," said Brodey.
Law enforcement sources told the paper that, as part of the same investigation, search warrants were served last year at the Hollywood Hills home of actor Paul Reubens -- best known for his character "Pee-wee Herman." Police seized an erotic art collection and personal computers at Reubens' home, but an attorney for Reubens said none of the items seized was anything more than erotic art.
Jones, who played Emperor Joseph II in the 1984 Oscar-winning movie "Amadeus," memorably played Mr. Rooney -- the dean of students in the 1986 hit comedy "Ferris Bueller's Day Off." He went on to play in dozens of movies -- including comedies such as "Without a Clue" and "Who's Harry Crumb?" and dramas such as "Valmont" and "The Hunt for Red October."
Jones has made three movies with director Tim Burton -- "Beetlejuice," "Ed Wood" and "Sleepy Hollow." Most recently, he has appeared in the 2001 comedies "Dr. Dolittle 2," "Heartbreakers" and "How High."
Celebrity Families of 2014 [PHOTOS]