Springbok captain Victor Matfield paid tribute to his side's staunch defence as the world champions withstood a late rally from Wales to win 25-29 at the Millennium Stadium.
The victory kept South Africa's hopes of a Grand Slam alive after they brushed aside Ireland last weekend.
South Africa were 17-9 behind at the break but scored 17 unanswered points in the space of seven minutes to grab the initiative from Wales.
Wales refused to cave in and mounted a fierce late rally but couldn't breach the green wall.
"I'm very proud of the boys, they showed great character," said Matfield. "Wales put us under pressure and it was a great game for the spectators to watch.
"Well done to Wales, they really came out and played well. "(Defending) is something we really worked hard on (in training) and it came through and we were happy with that," he added.
Referring to a possible Grand Slam, Matfield said: "I don't know. There's still a fair way to go. We're focusing on Scotland and that's going to be another huge game. We will enjoy tonight and then start fresh from zero on Monday again."
Wales U20 face a tough group in the Junior World Championship with France, England and Japan lying in wait but Attack coach Jason Strange and back rower Tom Phillips are looking forward to the campaign ahead.
Angus O'Brien has quickly settled into the Wales Sevens squad after solid performances in Hong Kong and Japan. With two rounds remaining in Glasgow and Twickenham on the World Series, WRU TV's Graeme Gillespie chats to the rising star.
Wales winger Luke Morgan has established himself as one of the deadliest finishers on the Sevens World Series. WRU TV's Graeme Gillespie catches up with him on the eve of this weekend's round in Glasgow.
All roads lead to Cardiff on Sunday for the SSE SWALEC Finals Day at the Millennium Stadium. Cambrian Welfare tackle Ystradgynlais in the Bowl final, Ystrad Rhondda play Newcastle Emlyn in the Plate final while defending champions Pontypridd face Bridgend in the Cup final.
WRU Chief Executive Roger Lewis, Deputy Minister for Culture, Sport and Tourism Ken Skates and WRU Chairman Gareth Davies earlier this week launched a new competition in conjunction with the WRU unveiling its archive room.
Welsh players and management joined Deputy Minister for Sport Ken Skates at the Pierhead Building, Cardiff Bay earlier this week to reveal the Union's pioneering school-club hub initiative has been so successful the project will now almost double the scale of the original project.
The Scarlets, Newport Gwent Dragons, Cardiff Blues and the Ospreys look ahead to Judgement Day III which sees the Blues take on the Ospreys (2.30) and the Dragons tackle the Scarlets (4.45pm) at the Millennium Stadium tomorrow afternoon.
Ystradgynlais and Ynysddu played out a titanic struggle at Taffs Well in the SSE SWALEC Bowl semi-final. At the end of the game neither team could be separated after a 15-15 stalemate but Ystradgynlais go through on try count.
Blues strike first in JD III battle - Newport Gwent Dragons lock Andrew Coombs, WRU referee Dylan Llyr Jones and Cardiff Blues hooker Matthew Rees decide dressing room allocations for Judgement Day III