Vilakazi sustained the injury during the national team’s practice game against SuperSport United at Megawatt Park on Wednesday morning.
Bafana won 1-0 through a goal by Lebo Mothiba in the first half.
Coach Stuart Baxter used a different team in the second half as he went about assessing all the players in camp.
Bafana take on Seychelles in back-to-back matches, with the first match pencilled in for Saturday at FNB Stadium, and the two teams face each other again next Tuesday on the Indian Ocean island.
South Africa are second on the log with four points, together with log leaders Libya, and the two upcoming games will prove crucial in shaping who will qualify for the 2019 AFCON tournament in Cameroon.
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