The Fire initially declined the option on Segares' contract on Monday, meaning he had become a free agent, but the Chicago club have backtracked on that and signed the Costa Rican to a multi-year deal.
"I'm very happy to continue on as a Fire player," he said in a statement.
"Chicago is my second home and the Fire have been a big part of my life for a long time. I look forward to more success with the club in the future."
Fire president of Soccer Operations Javier Leon added: "We're pleased that Gonzalo will remain a member of the club.
"He has been a tremendous asset to the Fire backline for nearly a decade and has been key to our defensive stability."