Archer, who burst onto the cricket scene at last year’s World Cup, pulled up with the injury in practice on Wednesday and was awaiting the results of the scan before England’s final practice on Thursday.
The second Test at Newlands starts on Friday with England 1-0 down in the four-match series after losing by 107 runs in Pretoria last Sunday.
“We are still waiting to hear back, results-wise, about his scan so we should know further today and then we’ll have to play it by ear,” Root told a news conference.
“It was quite disappointing to see him pull up like that and now we’ll just have to make another late call.”
Archer batted and fielded with the rest of the team on Wednesday but then after a few balls pulled out of bowling in the nets.
Archer’s affliction, which Root said might be an old injury, adds to the tale of woe the tourists have been subjected to since arriving in South Africa on Dec. 14 after 10 players contracted a flu virus.
“It’s been frustrating throughout, but these things happen in sport and you got to manage them as best you can and we are trying to do everything we can to make sure that if anyone does pick up illness or injury, others are fit and ready to go,” said Root.
The 29-year-old conceded that potentially losing Archer would be a major blow to England, seeking to get themselves back into the series at a venue where South Africa have rarely lost.
“If you look at his short career, he’s made impacts with big moments in big Test matches so, of course, it will be a big loss if he is not fit to play but it creates another opportunity for someone else,” Root said.
It could prove a reprieve for England’s record wicket taker James Anderson, whose tepid performance in Pretoria suggested he might be sacrificed for a spinner on what is expected to be a docile Newlands wicket.
But England were still some way off a final selection, Root added.
“Everything is still on the table as it stands. We’ll make a decision on the surface when we’ve had a closer look at it, maybe even tomorrow morning,” he said.
“With not knowing exactly how Jofra is, it might change the way we balance the side up.”