Marques confirmed the news after his side beat his former club Moroka Swallows 1-0 at Athlone Stadium on Sunday to ease their relegation concerns.
"I can say that I won't be back next season," said Marques, who was extremely animated on the touchline after People's Team skipper Tyren Arendse scored the winner from the penalty spot late in the game.
"It's a difficult decision but I thought long and hard about and it's a move I have to make. I won't be coaching any team soon but yes, I'm leaving the club at the end of the season."
Marques added: "It was an interesting season for me here in Cape Town and have learnt a lot you know.
"The diversity of Cape Town, the players and culture is something you have to keep in mind at all times. Of course things didn't go the way I anticipated but it was still a very good experience and learning curve.
"Santos is a passionate club with a strong family bond. It was a good experience for me as a coach."