Bartlett, a Bafana Bafana legend, guided Golden Arrows to the Absa Premiership last season by claiming National First Division honours.
Arrows, however, opting against handing the 43-year-old a new deal, and he later worked with the South Africa U-23 team in the run-up to their successful U-23 Africa Cup of Nations campaign in Senegal.
Troughton has been involved with AmaTuks for years, but departs with the club lying second-from-bottom in the standings with 12 points from 15 games.
Tuks CEO Dr. Rendani Mulaudzi thanked Troughton for his efforts.
"Though we are parting with coach Sammy in the middle of the season, we shall always hold him in high esteem for his loyalty and coach acumen for the many years he was an integral part of our programme," Mulaudzi said.
"We shall not forget the role that coach Sammy played in our structures for so many years, and we wish him the best as we part ways. We would like to thank him sincerely for the role he played in making our football programme and AmaTuks what they are today."
Bartlett will be aided by assistant coach Evangelos Vellios and goalkeeper trainer Tendai Tanyanyiwa. Their first assignment together is a trip to high-flying Platinum Stars at Royal Bafokeng Stadium on Sunday.