Morena is nursing a quad injury, which saw him removed from Sundowns' team sheet during their warm-up for yesterday's league game with Bidvest Wits at Lucas Moripe Stadium.
Downs coach Pitso Mosimane confirmed the setback after his side's 1-1 draw with the Students in Tshwane.
"It is sad," Mosimane said.
"He [Morena] was supposed to go to Bafana Bafana.
"I saw Seychelles against Nigeria and he was supposed to be the one to go down the line."
Following the injury to Morena, Mosimane shifted Motjeka Madisha across to right-back and brought in Wayne Arendse to feature in central defence against Wits.
It's a tough break for 25-year-old Morena, who recently won over Bafana coach Stuart Baxter after being left out in favour of Reeve Frosler and Ramahlwe Mphahlele for the Four Nations friendly tournament in Zambia in March.
At the time Baxter explained that Frosler was a better investment due to his age while Mphahlele offered more experience.