Marques was impressive in the single season that he spent in the Mother City keeping 17 clean sheets in 33 appearances for the club and ultimately finished as last season's Goalkeeper of the Season.
The 36-year-old has since so far this campaign conceded seven goals in just three games as Eric Tinkler's side experienced an underwhelming start.
Marques has signed a one-year deal with Petro de Luanda in Angola with an option to extend and will be playing CAF Champions League football.
Petro are the most successful club in Angola and regularly features in the CAF Champions League.
"Goalkeeper Hugo Marques is the latest face of Petro de Luanda to reinforce Alexandre Santos' options.
"Hugo Marques has represented Cape Town City for the last season and a half," read a statement from the club.
Marques had already previously spent six years playing in Angola for Kabuscorp SC and Clube Desportivo Primeiro de Agosto
He was born in Portugal but is of Angolan roots and has played regularly as first-choice for Palancas Negras in the past two years.
Marques could come up against his former employers in the CAF Champions League in October if both win their first-round ties.
City play AS Otoho of Congo while Petro must deal with Black Bulls from Mozambique.