The painting has sparked fierce debate about the balance between freedom of expression and the right to dignity.
Hundreds of ANC supporters protested outside the gallery on Tuesday.
The painting, The Spear, was defaced last week. It will also be removed from the Goodman Gallery’s website.
Under the deal, the ANC has agreed to drop its legal action demanding that the gallery remove the painting from its exhibition and the website.
The red, yellow and black acrylic painting showing Jacob Zuma echoing Soviet images of Lenin was taken down after it was covered in red and black paint.
On Monday, South Africa’s City Press newspaper said it was removing the image of the painting from its website following threats by the ANC.
In a joint news conference, ANC spokesman Jackson Mthembu said: “Maybe we should not have gone to through lawyers, we should have talked directly.”
Goodman Gallery director Liza Essers said: “I believe in the right to freedom of expression and the South African constitution.”
“Brett [Murray, the artist] is very saddened by the hurt that the painting has caused,” she said.
The ruling party said the painting was “rude, crude and disrespectful” towards President Zuma and wants all images of the painting online and elsewhere taken down.
In an affidavit served on the City Press newspaper, Jacob Zuma said: “The portrait depicts me in a manner that suggests I am a philanderer, a womanizer and one with no respect.”
President Jacob Zuma, who has four wives, has previously sued local media companies 11 times for defamation.
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