Motsepe, the founder and chairman of African Rainbow Minerals, is demanding 5 million pula (R6.7m) in damages for injury to his reputation.
The lawsuit comes after Sunday Standard published an article on April 1 headlined "New Jerusalem Vic Falls secret meeting scuttled".
In it, the paper claimed the Mamelodi Sundowns owner and his sister, businesswoman Bridgette Motsepe-Radebe, donated R22m to Dr Pelonomi Venson-Moitoi’s campaign ahead of the ruling Botswana Democratic Party’s elective conference held last month.
Venson-Moitoi is former president Ian Khama's ally who was challenging Mokgweetsi Masisi for the party's presidency.
Part of the article read: “By Friday, a team of Botswana Police Service officers were investigating a number of security companies which are allegedly being used to smuggle campaign money into the country.
"This followed unconfirmed reports that South African mining tycoon Patrice Motsepe, who is also brother to Bridgette, had donated R22m to Venson-Moitoi’s campaign, which had already been smuggled into Botswana.”
According to court papers, which The Star has seen, the South African mining magnate is of the view that the statement is defamatory and could imply that he acts illegally and is a dishonest businessman.
“As a result of the publication of the offending statement, the plaintiff has been injured in his reputation and has suffered damages in the amount of P5000000. In the premise, the defendant is liable to the plaintiff in the amount of P500 0000,” reads the court papers.
Motsepe’s spokesperson Sizwe Nzimande confirmed that the lawyers had laid defamation charges against the Botswana weekly.
“There is some legal action being taken but I can't go into details because the matter is sub judice,” Nzimande said.
However, Sunday Standard editor Outsa Mokone said they were yet to receive the lawsuit.
“We have not received any lawsuit from Motsepe. Maybe it's still on its way. Otherwise, when it arrives it will be treated like any other lawsuit,” Mokone said.
He added that Sunday Standard had received more information about the allegations he claims implicate Motsepe in the domestic affairs of Botswana and would do a follow-up article on Sunday.
In addition to the money, Motsepe is demanding that the newspaper publish, within five days from date of the court order, an apology on its front page and website.
The apology, according to court papers, must take up a quarter of the page and remain published for seven calendar days.
Motsepe wants it to have the following wording: “To the extent that the Sunday Standard has made statements on its website stating or implying that Dr Motsepe has behaved illegally and dishonestly, the Sunday Standard hereby unequivocally retracts all such statements and imputations, and unreservedly apologises that they were made.
"The Sunday Standard regrets any inconvenience caused to Dr Motsepe."
He also wants the newspaper to pay the legal costs. The case is before Lobatse High Court Justice Tshepo Motswagole.
In April, Botswana banned Motsepe-Radebe and Joburg socialite Malcolm X from entering the country visa-free after accusing them of being at the centre of an alleged plot to topple Masisi.
Following the ban, Lindiwe Sisulu, then the minister of international relations and co-operation, met with Masisi in Gaborone.
In a Facebook posting, Masisi said: “The special envoy conveyed a message reiterating the longstanding and excellent relations between Botswana and South Africa despite the recent media reports.”