The centre back, who won the first of his 107 caps 12 years ago, was omitted on Tuesday when coach Pitso Mosimane named his squad for the match in Johannesburg on March 26.
Mosimane refused to discuss Mokoena's omission at a news conference, telling reporters only "it is time to move forward".
Mokoena had been called up last month for a friendly win over Kenya but was left on the bench for the match.
At the time, Mosimane said he wanted to use the game to try out a new defensive combination and accused reporters of making too much out of Mokoena being left among the unused substitutes.
The 30-year-old missed a November friendly against the United States when Mosimane said he was giving Mokoena a break.
Steven Pienaar has been named as captain in Mokoena's place for the key qualifier where South Africa are seeking to extend their lead over Egypt at the head of the group.
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