The technical team are yet to discuss whether they will call up a replacement.
The Mamelodi Sundowns man sustained the injury during the national side's practice match against SuperSport United at Megawatt Park in Sunninghill this morning.
It was during the first half when Vilakazi went down under a seemingly innocuous challenge, but his reaction quickly indicated the situation was serious.
Vilakazi's Sundowns teammate Thapelo Morena and Orlando Pirates winger Vincent Pule have also been ruled out of the upcoming international assignments with injuries.
Bafana coach Stuart Baxter called up Cape Town City skipper Thamsanqa Mkhize and Sea Robbers attacker Thembinkosi Lorch as their replacements.
Bafana won the match 1-0 against SuperSport through a goal by striker Lebo Mothiba in the opening stanza.
Baxter used a different team in the second half as he went about assessing all the players in camp.
Bafana will first host Seychelles at FNB Stadium on Saturday (15h00). The return duel is three days later on the Indian Ocean island (15h00).
Bafana are second to Group E leaders Libya on goal difference with four points from two matches.
Nigeria have three points, with Seychelles yet to open their account.