Following a terrible start, the 36-year-old first baseman hit .308 with 27 homers and 80 RBIs in 84 games from June 27 on. That left him with a final average of .271 with 38 homers and 115 RBIs.
"Carlos is a key part of our plans for 2009, and we wanted to let him know as quickly as allowed that we wanted him back," Mets general manager Omar Minaya said in a statement.
"Yesterday -- the day following the conclusion of the World Series -- was the first day that we could pick up the option per the contract. It was our full intent to promptly close our deal with Carlos, and that's what we did."
New York had until next Wednesday to exercise the option. If the Mets had declined, they would have owed him a $4 million buyout.
Pedro Martinez was among six Mets who filed for free agency Friday, a group that included outfielder Moises Alou, second baseman Ramon Martinez and pitchers Tony Armas Jr., Luis Ayala and Ricardo Rincon.