Bafana looked destined for defeat after falling behind but produced a late response, with Teboho Mokoena converting a crucial penalty to earn Hugo Broos' men an important point and keep their knockout-stage ambitions alive.
Khumalo singled out Mofokeng and Makgopa for changing the momentum after being introduced from the bench.
Mofokeng replaced Jayden Adams at half-time and immediately added energy and creativity in attack, while Makgopa came on in the 66th minute for Iqraam Rayners and gave Bafana a stronger outlet up front.
"When are we saying 'wow'! He (Mofokeng) came on, he changed the game," Khumalo said on SABC TV.
"I said it, Makgopa will make a difference because when he gets the ball, it doesn't bounce back. He's the only striker that I saw after Mexico to be introduced. Out of five balls, he won four aerial duels in terms of playing him as a referral. He was holding it for the oncoming traffic."
Khumalo also urged supporters not to underestimate the value of the result, insisting tournament football is often defined by points collected rather than performances alone.
"At the end of the day, you say the point that you probably think is not worth having it is the one that will save your soul," he added.
"It's a tournament, a tournament is a journey, a marathon. So you don't disrespect what these boys achieved. And that's why I'm saying they can only build from what they've done."
With Mexico already securing qualification after defeating South Korea, Bafana now know victory in their final group match against the Asian side would secure a historic first-ever place in the knockout stages of the World Cup.