Majola also paid 4.7 million rand (then $540,000) to other members of CSA staff. The payments were not authorized by the national cricket body's finance committee.
Majola was permanently replaced at CSA by former International Cricket Council chief executive Haroon Lorgat in July.
Reacting to the court dismissing Majola's legal challenge, Lorgat told Eyewitness News in South Africa that "the sooner we can get the focus back to cricket, the better for all of us."
"What's important is we can bring closure to it," Lorgat said. "What has transpired over the last few years has not been good for cricket."
South Africa, the world's top-ranked test team, hosts India and Australia in series at the end of this year and the beginning of 2014.
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Follow Gerald Imray at www.twitter.com/GeraldImrayAP