The Pirates captain was shown two yellow cards in quick succession - in the 95th and 97th minutes - and will now miss South Africa's final group match against Rwanda through suspension.
Speaking on SABC Sport after the match, Khumalo described Mbokazi's red card as a moment of passion rather than indiscipline, saying the young captain had "taken one for the team."
"He took one for the team. He was ruffled, and he wanted to push - that I don't condone because it's retaliation. But you could see he was provoked, and his reaction came from frustration rather than recklessness," said the Bafana legend.
Khumalo explained that emotions were running high as South Africa pushed for a winning goal late in the game.
"The boy who provoked him started the situation. You could see the captain wanted the game to continue - he was angry because he wanted to play on and help his team win," he added.
Fellow analyst Hlompho Kekana, however, urged Mbokazi to manage his emotions better, especially given his leadership role at Pirates and growing influence in the national team setup.
"As the captain of Orlando Pirates, he needs to understand the emotions of the game," said Kekana.
Khumalo concluded by acknowledging that while Mbokazi's actions were bookable, they stemmed from a player desperate to give everything for his country.
"Your emotions take over - you want to win, someone provokes you, and it destabilises you. That's football," he said.