It was a match of three parts as England started well before being found completely lacking in the middle third of the match.
But a strong finish combined with handling errors from the South Africans allowed England back into proceedings before a disagreement between Robshaw and replacement fly-half Owen Farrell over whether to kick for the corner or to kick for points allowed the Boks to tick down the clock and hold on for the win.
The decision will clearly be the talking point after England fell to a second defeat in as many weeks against southern hemisphere sides, but the hosts were lucky to be in with a chance of winning the match after a shocking middle third to the match that should have seen South Africa put things beyond doubt.
That said, the hosts should be given credit for at least attempting to play a more attacking game and they made an incredibly bright start to the clash as Geoff Parling charged down a poor box kick from Ruan Pienaar and quickly earned the hosts an early penalty.
Flood missed the chance but made no mistake second time around after the South Africans were penalised just five metres out from their own try-line.
Perhaps mindful of the narrow margins that would likely decide the match, skipper Robshaw instructed Flood to again kick for the posts.
England took the deserved lead, having barely allowed the Springboks any possession during the first five minutes, but were quickly pegged back after a terrible piece of decision making from Flood.
The moustachioed fly-half had little to no support around him when he decided to run the ball from his own 22, inevitably running into attacking Boks from every angle and putting the hosts so much on the back foot that it was only a matter of time before Pat Lambie got the chance to level the scores with his first kick of the day.
Tom Youngs, thrown into the England squad for the Autumn internationals as a result of an injury to Dylan Hartley, had looked solid in the lineout against both Fiji and Australia but endured a dismal day at hooker as his throws consistently went astray.
And it was a lost line-out that allowed South Africa to level as Lambie slotted over an easy kick.
Flood and Lambie exchanged penalty kicks just a few minutes later after the tricky wet conditions led to binding errors at the scrum – one from Jannie du Plessis and one from Robshaw.
A missed attempt from Flood was followed by a third penalty from Lambie and it was beginning to look as though the whole match would continue in the same vein as South Africa trotted in for the interval three points to the good.
But the tourists, who had already racked up wins against Ireland and Scotland, started the second half in a much more positive manner.
Luck was also on the Boks' side as they scored one of the ugliest tries seen all weekend across the international programme.
Lambie’s grubber kick bounced back off England legs only for JP Pietersen to toe-poke the ball upfield. Tom Wood tried to collect the loose ball only to knock on and Willem Alberts was waiting to collect the ball and dive over the line for the only try of the match.
There could be an argument that Pietersen was offside and Alberts would definitely have been offside had Wood not knocked on straight into the South African number seven’s hands and the Television Match Official had little difficulty in awarding the try.
Lambie added the conversion as England looked more than a step slow and the worsening conditions made it tricky to keep hold of the ball.
But South Africa failed to capitalise on poor decisions and poor kicking from the England team as Manu Tuilagi came to the rescue for the hosts.
Two mesmerising breaks from the forceful winger revitalised a frustrated England side, who were lucky to escape a sin-binning to Ben Youngs after the scrum-half was involved in a tussle with Eben Etzebeth.
Back-to-back penalties from Farrell, brought on for Flood in the 46th minute, left England trailing by just four points heading into the final 10 minutes.
But it will be the last three minutes that are the most dissected as Farrell questioned his skipper’s decision to go for the three points instead of the corner after being awarded another penalty.
South Africa's solid defensive record suggests Robshaw’s call to kick for the points and then to try and get another kick in could have worked had Farrell not taken the time to disagree, wasting precious seconds.
The Springboks then played the clock perfectly, dragging their feet to the re-start before also taking their time in preparing for the resulting line-out.
England simply ran out of time to press for the winning kick and will be left to rue their shockingly poor middle third to the match as they prepare for an even tougher test against world champions New Zealand in seven days' time.