Moosajee takes over from Logan Naidoo, who handled the task temporarily after Goolam Rajah retired from the position in September after 14 years of service.
Moosajee's tenure begins on June 1, and his first assignment as manager will be South Africa's tour of England in July.
''It will definitely be to my advantage that I have worked closely with the team for the past five years,'' Moosajee said.
He admitted that although the post of manager differs from that of doctor to the team, he planned to approach it with the same enthusiasm as he has done so far.
The chief executive of CSA, Gerald Majola, congratulated Moosajee while announcing his appointment.
''We are delighted that Dr Moosajee has accepted CSA's offer to be national team manager. He is already part of the cricket family and should have no problem settling into his new role.
''Dr Moosajee has a great passion for sport, and we believe his experience and knowledge of cricket will hold him in good stead for this position,'' he said.
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