The Springboks spread their tries among Thomas du Toit, Cheslin Kolbe, Kurt-Lee Arendse, Grant Williams, Malcolm Marx, Jesse Kriel and Ben Jason-Dixon with Kolbe putting over five conversions in his new kicking role on Saturday.
England's tries were shared among their forwards with Ellis Genge, George Martin and Alex Coles scoring and Fin Smith converting.
England threatened to be overrun at Ellis Park as they went 17-0 down after 11 minutes but they fought back to reduce the deficit to three points at the break, only to be out-muscled in the second half.
The Springboks came storming out of the starting blocks with prop Du Toit barrelling over in the second minute.
A break by fellow front rower Ox Nche kept up a whirlwind start, allowing Kolbe to go over for a second try after sixth minutes.
The third followed quickly as the home sledgehammer continued with the pack again setting up the score and Arendse finishing off in the corner.
England found their confidence restored when captain Jamie George stretched over to dot down the ball but he was ruled offside after a TMO check.
The visitors finally breached Bok lines in the 35th minute when Genge took a quick tap penalty and powered over.
Before half-time the deficit was down to three points as Smith kicked a 50-22 and from the resultant line out lock Martin was able to also breach the defence.
South Africa were again on the front foot with scrum-half Williams sniping for a 44th-minute try, followed by a score for Kriel 12 minutes later as the forwards pounded away to put the hosts 31-14 ahead
With 12 minutes left, England lock Coles reduced the deficit to 10 points but hopes of a comeback were ended when centre Tommy Freeman and Guy Pepper were yellow carded, reducing England to 13 men for the final stages.
That opened the door for two more Bok tries for Marx and Dixon.
