The cartoon by Jonathan Shapiro, better known as Zapiro, depicted Zuma unbuckling his trousers as his political allies held down a woman representing Lady Justice.
"President Zuma did the right thing in withdrawing the case. This bodes very well for media freedom," Dario Milo, who represented the Sunday Times, told the paper.
"It is to be hoped that he swiftly withdraws his other 12 live cases against the media. This will send out an important signal that the president respects the right of the media to criticise his conduct."
The withdrawal ends a four-year saga that began in 2008 when Zuma sued for R4-million in damages to his reputation and R1 million for injury to his dignity.
Zuma recently dropped his claim to R100 000 and a demand for an apology.
The case was to be heard in the South Gauteng High Court on Monday.
Shapiro told the Sunday Times that he had "mixed feelings" about the withdrawal as he believed he would have won the court case "hands down".
"This is a vindication of what I was saying in the cartoon and it's a vindication of the Sunday Times for publishing it," Shapiro said. – Sapa