Firefighters were called out to Oscar Mpheta Road Endlovini Informal Settlement where the buses were ambushed.
Golden Arrow suspended bus services in the area citing safety fears.
The City of Cape Town Fire and Rescue Service spokesperson Tracey Whittaker says the incident occurred shortly before 6pm.
The seven firefighters in two vehicles were escorted in by cops, and the fire was extinguished by 6.30pm.
Golden Arrow’s Bronwen Dyke-Beyer confirms: “Two buses have been gutted in separate incidents in Khayelitsha since Sunday evening.
“A number of buses have also been stoned.
“We are very disappointed and concerned because we are simply trying to render an essential service to the community. At this stage the motive is unknown.”
Police spokesperson Lieutenant-Colonel Andrè Traut says a case of public violence and malicious damage to property have been registered.
“Two buses were set alight in Harare, one on Sunday and one on Monday,” he says.
“The circumstances are being investigated and cannot be linked to any specific protest action at this stage.”
Police on Sunday used stun grenades to disperse angry backyarders from Town Two Khayelitsha who erected shacks on City-owned land.
The City broke down the structures and obtained three interdicts against the invaders.