Ibrahim was forced off in the Group B tie after scoring following a strong challenge from Nthethe at Petrosport Stadium in Cairo.
The 24-year-old has since been ruled out for three months with a broken fibula and dislocated ankle.
Nthethe hopes Ibrahim makes good progress with his rehabilitation.
"From Mamelodi Sundowns Football Club, and myself Thabo Nthethe, we just want to wish Mohamed Ibrahim a speedy recovery," Nthethe said in a video message released by Sundowns on Twitter.
See the short video below:
Downs, who won the game 2-1, will host the return leg at Lucas Moripe Stadium on July 27 needing a point to advance to the semi-finals of the competition.