Miguel Silva broke the deadlock with his goal just two minutes into the second half and Iqraam Rayners sealed the result with his goal after 59 minutes.
While Sundowns moved back to the top of the Betway Premiership with the three points, Orbit ended the evening in 15th place on the league standings, just five points clear of bottom-side Magesi.
Speaking after the game, a downbeat Makhoye admitted the result was disappointing after a strong performance in the first half.
"We had a good game plan especially first half, we applied ourselves well, until second half we gave them soft goals, he said on KickOff.
"I mean, we were on the counter in your half and we decided to go back to the keeper and that was a gift goal.
"And the free-kick, we had a lapse of concentration and they scored from that. So, it was always going to be the case because of now we have to fight to get another one unfortunately we conceded a penalty. I think it's one spot where those lapse of concentration."
The last time these two times faced each other Orbit also lost 2-0 but Makhoye felt his side acquitted themselves much better this time around.
“Compare to the first game when we played them, I think today we came and competed. I'm happy we know we're playing a quality side so even though the quality we have it's not the same,” said the head coach.
"Like I said before, the one-versus-one - the other one would be 90 and the other 100 (percent) that's the difference between us and them. But we keep soldiering on.