A finalist at the 2008 Beijing Olympic Games, Nhlapo took a cautious approach in his first three of five runs.
Nhlapo was tipped as a strong contender for a medal after he crashed out of the final four years ago and seemed to play it safe this time around.
"I made it pretty hard for myself and like I said, it was the top 32 guys in the world and it was going to be hard from the get-go," Nhlapo said on Thursday.
"I just managed to stay safe, but this weekend staying safe isn't enough," Nhlapo said. "I've been through so much the past four years. I've kind of learnt from my mistakes and I can sort of see something happens before it does."
While Nhlapo was the epitome of consistency – finishing fifth place in three of his runs and sixth in the other two – it was not good enough to secure a spot in Friday's semifinal.
But he did well to stay out of harm's way on three occasions where competitors crashed in front of him, with Nhlapo having to maneuver his way through the chaos.
Up against champions
In his second last run, Zabala Oquendo of Colombia crashed in front of the South African on the last bend, with Nhlapo doing well to avoid the fallen biker.
The 25-year-old also said the odds would always be stacked against him riding against defending Olympic champion Maris Stromsberg of Latvia and world champion Sam Willoughby of Australia.
"In those three situations when three guys fell in front, I managed to get around but then ended up getting passed," he said. "It's just one of those things, the safest place is out in front and when you've got the current Olympic champion and the world champion in your moto, it is a tough feat to do."
The last four years have been a see-saw in terms of injuries for Nhlapo, as he had to recover from a neck injury – fracturing two vertebrae in 2009 – and reconstructive knee surgery last year.
"I can't thank everybody enough for supporting me up to this point and sorry I couldn't make you guys proud," he said. "I'm just going to take some time off, let the body heal … I've really pushed my body hard just to get to this point with the injuries I've sustained over the past two years and I think it is just time to have a good rest and have a proper recover and focus on the next four years."
Nhlapo said he would turn his focus to the 2016 Rio Games after his break.
"I still have another four years still in me … I am only 25, a BMX rider lasts roughly till 32 so I think I've got a good six years left in me," Nhlapo said.
He added that South Africa had to invest more in the sport as the rest of the field were much better prepared.
"At this Olympics alone we have three countries that had built replica tracks like this at their Olympic training centers," he said. "I think South Africa has a long way to go in terms of producing future champions and future Olympians and hopefully they can pick up the pace and learn from what the other countries are doing." – Sapa