A brutal finish in the 43rd minute by blind-side flanker Risima Khosa, part of an all-Lions back row, showed there would be no South African complacency.
But back came Wales after wing Cheswill Joose – going up against fellow United Rugby Championship (URC) breakthrough prospect Bowen – was sin-binned for a deliberate knock-on.
The TMO denied lock Will Evans a try after spotting a knock-on but Leggatt-Jones put Darwin-Lewis over and converted to make it 33-21 with half an hour to go.
South Africa responded with another try from a driving line-out, this time by replacement hooker Liam van Wyk, before a Welsh cracker by Bowen from Darwin Lewis’ offload.
That score earned Wales a bonus but the spoils were secured through another driving score by Van Wyk that made it 45-26 in the 62nd minute.
A similar try followed by Mnebelele as South Africa passed a half-century before Wales finished on the front foot and scored their fifth through full-back Edwards with the help of a two-man advantage.
Wales Under-20s head coach Richard Whiffin said: “I’m incredibly proud of the boys. We spoke about swinging the bat and we certainly saw that, scoring five tries and having two disallowed.
“We were brave with the ball but the Junior Boks were very clincial when they got in the 22.”
Wales Under-20s: Lewis Edwards (Ospreys); Rhys Cummings (Cardiff), Osian Darwin-Lewis (Cardiff), Steffan Emanuel (Cardiff), Tom Bowen (Cardiff); Carwyn Leggatt-Jones (Scarlets), Sion Davies (Cardiff); George Tuckley (Dragons), Tom Howe (Cardiff), Jac Pritchard (Scarlets), Will Evans (Scarlets), Tom Cottle (Cardiff), Deian Gwynne (Gloucester, capt), Caio James (Gloucester), Evan Minto (Dragons).
Replacements: Oscar Thomas (Bath), Dylan James (Ospreys), Yestyn Cook (Scarlets), Luke Evans (Exeter), Osian Williams (Bristol), Alex Ridgway (Bath), Cai Gealy (Bristol), Lloyd Lucas (Cardiff).
Yellow card: Pritchard 30.
