Orbit's Betway Premiership fate was confirmed after a 2-0 loss to the Buccaneers, while Magesi secured a crucial 1-0 victory over Richards Bay to survive and condemn the newcomers to the drop.
Makhoye, who has been part of Orbit's journey since the club's formation, admitted the two own goals against Pirates proved costly, but insisted the experience would ultimately help both him and his young squad grow stronger.
"Not the result we wanted and, like you said, those two mistakes changed the whole half-time talk because we conceded right when we needed to go for the (half-time) break," Makhoye told the media after the game.
"When we came back, we conceded early again when we lost a player through injury so we were still one man short, and unfortunately we were supposed to clear the ball outside.
"We cannot fault these young boys, they gave a good performance and I'm proud of them. We've been building this young team for the past six games and I think we are growing."
The Orbit mentor revealed the club had prepared for every possible outcome before kickoff, including the prospect of returning to the Motsepe Foundation Championship (MFC).
"Unfortunately today (Saturday) they (players) knew it's either the playoffs or we get relegated straight, and we prepared for any situation that would come," he explained.
"We are going down, we have to accept that and move on, and prepare for next season."
Makhoye also pointed to his decision to field several under-23 players as part of planning for the future.
"Even today I started with around four under-23 players so it means I was preparing for life in the MFC if things didn't go well for us," he added.
"Indeed it happened like that, but we've learnt a lot this season and if we get another chance to get promoted again, I'll be calmer in this league as an experienced coach because I had to learn somewhere."