Motlanthe "was never involved in assisting 360 Aviation to obtain the support of the South African government for the business transaction involving the Islamic Republic of Iran," according to Madonsela's report released on Friday.
Motlanthe asked the public protector to investigate after a Sunday Times report on March 11 2012.
The report alleged that Motlanthe's partner, Gugu Mtshali, was "implicated in soliciting a R104-million bribe to obtain a sanctions-busting deal with Iran".
The article said Mtshali had met associates of Motlanthe and representatives of 360 Aviation, at a restaurant in Bryanston, Johannesburg, in February 2011, "to discuss buying government support" for 360 Aviation.
The company allegedly planned to trade aircraft in Iran. At the time there were United Nations-imposed sanctions against Iran, which included an arms sales embargo.
The public protector said Mtshali attended part of that meeting, and uttered only the words: "No! … Hey man Jo, c'mon Jo …"
"Ms Mtshali's presence and utterance of the above few words do not substantiate a finding that she participated in the meeting or the Iranian deal, or solicited and/or accepted a bribe or gratification in exchange for influencing the government of South Africa to support 360 Aviation's Iranian business venture," the protector found.
Motlanthe welcomed the report.
"The report of the public protector repudiates the statements made by Mr Barry Oberholzer, and published in the Sunday Times on March 11 2012, alleging improper conduct by the deputy president and his partner Ms Gugu Mtshali," his office said.
"The public protector found no evidence suggesting that either deputy president Kgalema Motlanthe or his partner were involved in any business transaction with Mr Barry Oberholzer."
"Mr Oberholzer, in his interview with the office of the public protector, asserted that he had never met nor had any business relations with the deputy president and his partner," it said.
"It is worth noting that the public protector found that there were 'material differences in the words supposedly uttered by Mr Mboweni and Ms Mtshali as reflected in the transcript, when compared with the recording made by Mr Oberholzer'."
"It is not clear whether Mr Oberholzer or the Sunday Times deliberately distorted the transcript in order to mislead the public about Ms Mtshali's conduct," the statement said. – Sapa