At least seven people died in the unrest, which badly strained relations between South Africa and many countries in the region that were outraged at the targeting of their citizens.
In what African Union analyst Liesl Louw-Vaudran said was an unusual move, the subject of xenophobia will be tackled in a closed session before the opening ceremony on Sunday morning.
The session will also discuss migration -- and will likely focus on the flood of African and Middle Eastern migrants trying to cross the Mediterranean.
Mass drownings have claimed nearly 1,800 lives so far this year, according to the International Organization for Migration