United Cricket Board of South Africa spokesperson, Gerald DeKock, said that Boje had taken the decision because he didn't want to find himself in an awkward position in India.
"The Indian police had not been able to give him any assurance despite the fact that he had answered a questionnaire from the Indian police and had supplied documents from the King Commission of Inquiry", said De Kock.
De Kock said Carl Langevdldt would take Boje's place in the team.
Another player, opening batsman, Herschelle Gibbs, had withdrawn from the team a few weeks ago after he had expressed his misgivings about being arrested and detained in India.
Boje and Gibbs had been implicated by the late former cricket captain, Hansie Cronje, as being involved in the match-fixing saga during South Africa's tour in 2000.