The Blitzboks were in imperious form
heading into Sunday's decider, but tries from Richard de Carpentier, Dan Norton and Ruaridh McConnochie were enough to give England a narrow victory.
A total of 108,941 fans attended Cape Town stadium over the two days of action and, while it wasn't the result the home fans were looking for, the drama undoubtedly provided value for money.
Trailing 12-5 at halftime, South Africa -- which had won its home tournament for the past three years -- flew out of the blocks and leveled the score soon after the restart.
England, without a tournament win since Tokyo in April 2015, rallied and McConnochie went over to restore its lead.
In a dramatic finish, Werner Kok scored as the final hooter sounded and Justin Geduld was given the unenviable task of making the conversion from wide on the touchline to take the match into extra time.
However, Geduld hooked his kick wide of the posts and a jubilant England team celebrated as it climbed to within two points of South Africa at the top of the standings after two rounds.
"It was a tough tournament, to back up last weekend (reaching the semifinals) I am so proud of the boys," England captain Tom Mitchell, who led Great Britain to a silver medal at the Rio 2016 Olympics, told World Rugby.
"We trained all summer and this makes it all worth it. We were a bit disappointed last weekend and we wanted to put it right.
"It's been a bumpy road but it always is. It was a pleasure to play in this stadium."
The next round takes place in Wellington on January 28-29, and 12-time series champion New Zealand prepared for its home leg with a hard-fought 24-19 win over Scotland in the third-place playoff.
Although disappointed not to make the final, the 14-7 semifinal defeat to South Africa was a stark improvement on the 40-point hammering New Zealand received last weekend in Dubai.
Scotland, which lost 33-14 to England in the semis, led twice in the playoff. However, a try from Jonathan Ruru in the dying seconds ensured New Zealand remained unbeaten against its opponent for 36 games.
Olympic champion Fiji
, seeking its third successive world series title, finished fifth after losing 31-26 to England in the quarterfinals.