Jali, who is part of the country's provisional squad, was diagnosed with a mild cardiovascular problem on Friday.
BBC: South African Andile Jali ruled out of World Cup
But coach Carlos Alberto Parreira said he would take no chances with Jali.
Jali made his international debut earlier in the year and the mild cardiovascular condition was detected in routine tests on the 30-man squad.
Midfielder Andile Jali, who was originally part of the provisional squad, was diagnosed with a mild heart condition that ruled him out of selection on 23 May.
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