Head coach Mike Friday accepted his team had been outplayed as they conceded three tries to a far more experienced outfit.
But he was left fuming after Welsh referee James Jones failed to take any action against South Africa's Danwel Demas for what appeared to be a high tackle on Harlequins winger David Strettle.
Friday insisted the tackle deserved a straight red card - and his frustration was then compounded when captain Simon Amor was sin-binned for dissent.
"It was late, high and intentional and there were punches thrown afterwards," said Friday.
"At that stage it was just 7-0 and it was a key moment in the game because they could have been down to six or even five men because of the punching.
"Simon will be disappointed with his sin-binning but it bemuses me how officials can clamp down on dissent harder than on dangerous play."
England had beaten Australia 21-5 to reach the last four but the tone for the semi-final was set in the opening five minutes by South Africa's solid defence.
They kept England at bay and then struck just before the interval when Philip Burger escaped through Andy Vilk's tackle.
In horrendous conditions, the South Africans then worked England around the park well, creating space for Ryno Benjamin to sprint onto two cross kicks and seal the win.
England may have let their title slip but Friday refused to be too downhearted by the result.
His squad contained seven new caps and he was able to identify positive signs heading into next weekend's tournament in George.
"South Africa are a very balanced side," said Friday. "They have been together as a squad for two years, while we had seven new players getting their first taste of Sevens.
"It was a useful experience for us."
South Africa claimed the title after recovering from 12-0 down at the interval to score five second-half tries and beat New Zealand 31-12.
Samoa won the Bowl, Argentina claimed the Plate and Wales left Dubai with the Shield after Cardiff's Tom James scored a hat-trick in a comprehensive 33-0 victory over the Arabian Gulf.
Wales would have qualified for the Cup quarter-finals last night if New Zealand had not been upset by Samoa, so the eventual result - 13th out of 16 - was a disappointment for coach Dai Rees.
But in front of Welsh Rugby Union chief executive Steve Lewis, Wales pulled off a big win over Samoa and only lost to established Sevens nations New Zealand and Argentina all weekend.
Rees said: "Some people at home don't quite understand what a great development tool Sevens is. That doesn't matter to me as long as we continue to develop the players.
"We had James Hook last year and players like him only arrive once every five or 10 years. But we have also lost five or six others who came through Sevens and have now established themselves with their regions, players like Tal Selley and Aled Brew.
"It was great that Steve Lewis was out here and he has been impressed with what he has seen.
"We were disappointed to be in the Shield but the boys went on a steep learning curve this weekend."