Mkongi made the call via a Facebook post and has since apologised for the post and retracted it.
"Comrade Mkongi has stressed that he harboured no intention to either harm or cause violence, and has since publicly retracted and apologised for the post.
"Indeed the provocative and inflammatory banner was taken down peacefully. We have accepted the retraction and apology and no further action against him has been decided," said spokesperson for the office of the ANC chief whip, Moloto Mothapo, in a statement.
'Burn to death'
In his post, which led to a social media outcry, Mkongi said, "Join the ANC in Cape Town today [Saturday] at 14:00 to burn down the billboard saying 'ZumaMustFall'. The billboard must not be lifted down, but, burnt down."
One person commented, "We can't burn it down as it is pasted against an apartment block, people inside the apartment will burn to death. We can remove it though."
Mkongi responded with,"They must burn to death as it is life for them to keep it that way."
Mothapo said, "The gigantic and expensive billboard, sponsored by the privileged and wealthy racists of the DA, had all the malicious intent to racially polarise and incite political tensions with a view to distract public attention from the increasing levels of racism both inside and outside the ranks of the DA.
"The DA has been pulling all the stops to defend and justify racism and promotion of apartheid amongst its membership, and has thus sought to create an expensive stunt to deflect from the negative attention it has been suffering."
The DA however, which has repeatedly been calling for President Jacob Zuma to step down, has denied having anything to do with the banner.
'It isn't ours'
"It isn't ours," DA spokesperson, Phumzile van Damme, said with a chuckle when questioned about her party's involvement at the weekend.
Mothapo however, said the DA's involvement was confirmed when party leader, Mmusi Maimane, was reportedly asked by a Johannesburg-based radio station whether his party was responsible for the billboard.
"He said he could 'neither confirm nor deny' – a response that is generally understood to be affirmative," said Mothapo.
He also criticised the City of Cape Town for allegedly doing nothing to stop the illegal act from being carried out.
"Instead of dispatching the Metro Police to stop the public violation of its laws, all it did was to issue a media statement," said Mothapo.
He said it seemed as though the deal struck between the DA and the City was that the City would denounce the banner and eventually instruct its removal within a period determined by the City itself but the impact would already have been made.
He said the underhanded tactics were bound to backfire.