The Rockets took a 43rd minute lead at the New Peter Mokaba Stadium through a Jean Lwamba Lubumba own goal.
Mfanafuthi Mkhize equalised in the 58th minute and Lubumba made up for his earlier error with a 71st minute winner.
Keet, who joined City at the start of the season, played his part with a commanding performance between the poles and after the game, announced his plan to call it quits at the end of the season.
Speaking after the match, an emotional Keet explained what the trophy meant to him and his family.
"Obviously it's special," he said on iDiski Times.
"You know, my parents have been there, obviously throughout my whole career. My dad's never really been one to be involved, so it's nice for him to enjoy these moments, for them to enjoy my last trophy. And I'm hoping they enjoyed it.
"My dad cried a bit. I haven't cried yet, but when I saw some of the players crying, then you feel like crying also.
"But happy tears at the moment and happy smiles at the moment, but very special for me to have my family and my parents and my wife and my kids just awesome, awesome experience overall.
"I'm not hinting at anything, I'm calling it quits at the end of the season. So Nedbank Cup was my first and Nedbank Cup is my last [trophy]."
As a result of their cup success, City will play in the CAF Confederation Cup next season.
