The animals are shot by monitors who shadow the city's several primate troops, which are notorious for causing havoc in areas bordering their natural mountain habitat.
"It does work, it's actually fantastic," said city veterinary scientist Elzette Jordan.
"They hate it so much, so when they just see you with it and you shake it and they hear the paintballs rattling inside, then they move off already, and you don't actually have to shoot."
The paintballs are being used alongside other aversion techniques while a baboon management road map is drawn up.
Paintballing is the most common technique and its success is attributed to the apes not liking projectiles being hurled at them.
However, some street-wise animals have learned to spot white paint and duck when it is fired, forcing monitors to use more colourful options.
Cape Town's mountainous peninsula is home to several protected Chacma baboon troops and bold plunders are frequent. People have been injured in some instances.
"Our current strategy is to get them 100% out of urban space," said Jordan.
"We want to push them back into the natural space and for us to do that, we have to teach them that they can never be quite sure and feel safe inside the urban space and that's why we're using aversion conditioning techniques."
The paintballs were first trialled at the beginning of the year. – Sapa-AFP