Flames were seen billowing from the building's roof on Monday, as firefighters tried to douse the blaze.
The fire first broke out on Sunday and completely destroyed the National Assembly, or lower chamber.
Police have arrested a suspect who will appear in court on Tuesday on charges of arson, housebreaking and theft.
Authorities had warned that flare-ups would be possible because of carpets and wooden floors in the building, with parliamentary spokesman Moloto Mathapo telling South Africa's TimesLive some firefighters had "worked throughout the night" to try and prevent further blazes.
But just 12 firefighters were on site when the wind reignited wood above the National Assembly on Monday, according to news agency AFP. Despite reinforcements being sent, flames could still be seen emerging from the building as night fell.
An update from the city council at 22:00 local time (20:00 GMT) said the building's fourth and fifth floors had been completely destroyed. It was not immediately clear if the blaze had been extinguished.
On Sunday, President Cyril Ramaphosa - who admitted the building's sprinkler system had not functioned properly - praised firefighters for responding to the "terrible and devastating event" in minutes.