Orlando Bosquete, 52, was headed to a detention center where he was to be charged with violating immigration law, Immigration and Customs Enforcement spokeswoman Barbara Gonzalez said.
He will have the chance to present his case to a judge, who will decide if he can be deported, Gonzalez said. She declined to discuss specifics of the charge.
The arrest came after Circuit Judge Richard G. Payne said that DNA evidence proves Bosquete was not the man who sexually assaulted a Key West woman in 1982.
Before Tuesday's arrest, Bosquete expressed frustration at his extended incarceration, but said he was glad he was proved innocent of the rape.
"It is very important to me to forgive because I have to start a new life," he said.
Bosquete's lawyers said he came to the United States from Cuba in the 1980 Mariel boatlift where more than 125,000 Cubans fled the communist island.
Bosquete, who escaped from prison twice, is being represented by the Innocence Project, a nonprofit group is based in New York. His lawyers said the immigration confusion comes from charges he pleaded guilty to under aliases he used while an escaped convict.
Bosquete was arrested shortly after the 1982 assault when the victim, sitting in a police car, identified him from 20 feet away as her attacker.
Bosquete escaped in 1985 and wasn't re-arrested until 10 years later. He escaped again three months later and was at large for a year.
Prosecutors in Palm Beach County dismissed his 1985 escape charge on Monday, and Bosquete has served the sentence he got for his second getaway, officials said.