The tourists lost seven wickets for 49 in just over an hour to slump to a 280-run defeat in Centurion, as Kagiso Rabada ran riot for the second innings in a row.
England will rightly celebrate a 2-1 win over a Proteas side who went into the series as the world’s number one team, but there are major question marks over several of the side.
Joe Root, Ben Stokes and Jonny Bairstow have all excelled with the bat but their efforts have not been matched elsewhere in the order.
Cook has been among the strugglers but, as he closes in on 10,000 Test runs, his credentials are not in question.
The same cannot be said of Alex Hales, James Taylor or Nick Compton.
All three have ended the tour on a low note - averaging 17, 26.57 and 30.62 respectively - and cannot be certain of lining up when England welcome Sri Lanka in May.
And Cook did not sugar the pill when he assessed the trio’s performances.
“It’s been tough batting conditions and it’s not been easy, but there are still a lot of unanswered questions in our top seven batting,” he said.
“I think at the end of the day results matter and your end column of runs is absolutely vital. So to say they’ve totally convinced me would be wrong, but there have been flashes.
“There’s certainly places up for grabs. Myself and Trevor (Bayliss, head coach) and the selectors will have to sit down and discuss that because the output we’ve had in this series hasn’t been good enough if we’re trying to get to number one in the world - which is the ultimate aim.
“We have to produce better numbers than that and that’s myself included in this series.
“That will be discussed and those guys have got to continue working hard and make sure when selection comes round for Sri Lanka they’ve got a bucket load of runs for their counties.”