The former Mamelodi Sundowns and Orlando Oirates defender helped Callies win promotion to the GladAfrica Championship after guiding the team up from the ABC Motsepe League.
Troughton has now been replaced by Joel Masutha at the Romans, according to a source close to the club.
"The club has parted ways with Sammy Troughton" confirms a reliable insider. "He has since been replaced by Joel Masutha."
Callies are currently chasing the Nedbank Cup trophy after qualifying for the semi-finals, where they will meet Chippa United.