The 24-year-old Spaniard featured only seven times for the Addicks and spent last season on loan at the Belgian top-flight club.
A product of Barcelona's academy, he joined Tottenham at the age of 18 but was released in 2015 after failing to make a first-team appearance.
Ceballos played just 301 minutes for Charlton during the 2015-16 season.
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Charlton Athletic winger Cristian Ceballos has joined Sint-Truiden on a three-year contract.