Fly-half Johan Goosen slotted five penalties while centre Paul Jordaan contributed eight points via a try and a penalty.
So after three years and 19 straight wins, England Under-18s were finally adjusting to the reality of defeat and Fletcher was left to rue his side's lack of cutting edge.
"We just lacked precision and although we scored three tries to one we left a couple of straightforward ones out there and that's hard to take," said Fletcher.
"You couldn't fault us for effort and we had enough ball and enough chances to score but that's how it goes.
"Great credit to South Africa - they really hung on in there - and their reaction tells its own story.
"They got out of jail and are incredibly pleased to have beaten us. It shows the regard we're held in. We expect to win and that wasn't the case a few years ago.
"Our lads are very upset and it shows how much they care about the loss but we'll all move on and they will learn from it which is the important thing. It's been a great trip and they've conducted themselves brilliantly."