Ronald Fischer was captured without incident about an hour off New Jersey after authorities intercepted his 56-foot sailboat, The Silver Lining, state police said.
A multi-state operation involving Rhode Island's fugitive task force, the FBI, U.S. Marshals and the Coast Guard tracked the vessel, which was registered under the alias Richard Graydon.
Fischer vanished in 2005 during his Newport rape trial, leaving a "Goodbye" email to his lawyer, and was later convicted in absentia of first-degree sexual assault.
The 70-year-old former doctor had been on Rhode Island's most-wanted list for more than two decades, with investigators describing a worldwide search tied to more than a dozen aliases.
Authorities transferred him to U.S. Marshals custody in Staten Island and said he will be returned to Rhode Island to face the sentence he evaded.