The duo are now contracted to the reigning Telkom Knockout Cup champions until 2021
City made the announcement on their official Facebook page on Wednesday morning.
"Cape Town City Football Club can officially confirm that key players Lebogang Manyama and Aubrey Ngoma have signed new long term deals that will see them in the Blue & Gold until the 2020/2021 season," a statement read.
City club chairman John Comitis stressed the importance of keeping their best players in order to continue challenging for major trophies.
“With the ambitions and exciting plans for Cape Town City in the near future, it was an easy decision for Aubrey and Lebo to stay, as they are determined to play integral parts in this journey," Comitis said.
"Our players are at the top of their game because they are happy, motivated and love the club. The team plays for one another and therefore plays without fear.
"When “in-demand” players like Aubrey and Lebo make a statement and long-term commitment like this you begin to understand just how powerful and unified this team is becoming," he continued.
"This sends a clear message that Cape Town City FC is a club for the future. One that strives to play a dynamic brand of football, keeping the talent necessary to compete for trophies every season. The idea of "cashing in" is not part of our strategy.
"We are not a selling club, we are here to win. Our fans and trophy cabinet are what is ultimately important as we strive to bring fan culture and pride back to the mother city,” he concluded.