Since landing in the country a combination of sickness and flu-like symptoms have floored the squad, with 11 players and a handful of support staff falling ill before, during or immediately after the first Test defeat in Centurion.
Archer had missed both warm-up games because of illness.
Having finally left those problems behind them in Johannesburg the squad celebrated the arrival of 2020 together and were ready to train as a full group for the first time since at Newlands on New Year’s Day.
All 19 players were present at the ground but Archer was unable to bowl due to soreness in his right elbow, immediately placing a question mark over his availability.
The 24-year-old joined in fielding drills and also batted but would need to take a full part in the final preparatory net sessions in order to prove himself ready for the rigours of a five-day clash with the Proteas.
Should Archer not be passed fit, and the current indications are that he is not expected to bowl on Thursday (today), England will be without their quickest bowler, who took five wickets in the second innings at SuperSport Park.
On the other hand it would spare captain Joe Root and coach Chris Silverwood a potentially awkward selection dilemma, giving James Anderson and Stuart Broad another chance to prove their enduring class.
England have gone in without a specialist spinner for their last two Tests but are likely to lean towards a shift in policy at Newlands, with Dom Bess pushing hard to earn his third Test cap after initially arriving as cover for the unwell Jack Leach.
With all-rounder Sam Curran performing impressively in the series opener, as well as offering variety as a left-arm swing bowler, that appeared to put one of Anderson or Broad in the firing line.
It would be a bold call to ditch either man, who share 285 Test caps and more than a thousand wickets, and that may now be a conversation for another day.
Jonny Bairstow is set to make way for the returning Ollie Pope, meaning Jos Buttler will retain the wicketkeeping gloves and bat at seven.
Buttler had a modest 2019 in Test cricket, averaging just 25.10, and has not proved able to find his best tempo against the red ball.
A dynamic, innovative star of limited-overs cricket, he is often a more prosaic player in his England whites but could be set to follow the lead of opposite number Quinton de Kock, who was named man of the match last time out after two risky but match-shaping knocks.
“You look at the opposition and Quinton played a really good knock and put pressure back on bowlers,” said Buttler.
“He tried to take the initiative and certainly, watching that from behind the stumps, that resonated with me.
“I feel like I’m not quite performing to the standards I need to and I’m trying to improve that and affect the game in positive ways for England.
“It’s certainly something I’m trying to work out.
“I think you can do a lot of work in the nets but I’m spending a lot of time thinking about the game when I’m sat in my room or trying to visualise things or work through them in my head.
“For me moving forward I’ve got to play the situation, as I’ve said, but I will try to be a bit more positive.”