The 39-year-old designated hitter agreed in January to a contract with a $14 million salary for 2019 and the club option.
He hit .311 with a team-high 41 homers and had 108 RBIs in 120 games. He spent two stints on the injured list for a wrist problem that led to a torn tendon. Cruz was 2-for-10 with a solo home run as the Twins were swept by the New York Yankees in the American League Division Series, and the Twins said after that series they planned to exercise the option.
Cruz would have received a $300,000 buyout if the option had been declined and would have become eligible for free agency.