Alexander Frederic Proctor, 58, was charged Wednesday with interfering with commerce by threat of violence for allegedly breaking out a window in the journalist's car and leaving a dead fish and a rose inside.
Times spokesman David Garcia said Wednesday the newspaper was "very pleased with the announcement of today's arrest. The safety of our reporter has always been our greatest concern."
Proctor has a record of burglary and narcotics arrests, and organized crime investigators from the FBI and Los Angeles Police Department are continuing to look into his background.
Proctor was lodged in the downtown federal Metropolitan Correctional Center pending his arraignment on Monday.
The Times said its reporter, Anita Busch, had been working on a story about the reputed plot by individuals linked to New York's Gambino crime family when the alleged threat occurred. Segal's former partner was eventually arrested in the alleged extortion.
Proctor was accused of breaking into Busch's vehicle, which was parked near her home, in June and leaving the fish inside with the rose in its mouth. He also allegedly left a note on the windshield with the word "stop" written on it.
Although Proctor apparently had no known mob connections, investigators believe his actions were aimed at scaring Busch off the Segal story.
"The only word he used was 'stop,'" Assistant U.S. Atty. Daniel Saunders told the Times. "I think it is pretty clear."