Pope made 56 not out as England struggled to 262 for nine on a day when the tourists, 1-0 down in the four-match series, failed to take advantage of what looked like a good batting pitch.
Before Pope prospered in a unbeaten last wicket stand of 28 with James Anderson after six England batsmen perished for scores between 29 and 47.
England’s problems were a tribute to the pressure exerted by the South African bowlers, who shared the wickets. Vernon Philander, Kagiso Rabada, Anrich Nortje and Dwaine Pretorius took two each, while left-arm spinner Keshav Maharaj kept a tight rein on the batsmen while sending down 27 overs and taking one for 68.
South Africa thought they had completed a highly satisfactory day when Pope was caught by Philander off Rabada shortly before the close with the total on 261 – but a review by the umpires showed that Rabada had sent down a no-ball.
The day after his 22nd birthday, Pope, who missed England’s 107-run defeat in the first Test in Centurion because of illness, played a composed innings and shared a 58-run fifth wicket partnership with Ben Stokes which threatened to break the South African stranglehold.
Stokes reached 47 on the ground where he made a career-best 258 four years ago and was striking the ball crisply before he hit an awkward drive against the pace of Nortje and was caught at cover.
The innings then changed dramatically as Jos Buttler and Sam Curran fell before the second new ball was taken – and Dom Bess and Stuart Broad were dismissed in the first two overs with the new ball. From 185 for four England were 234 for nine.
But Pope was able to keep most of the strike, while Anderson was able to keep out the deliveries which he had to face.
England’s struggles were epitomised by captain Root. He had an escape on 31 when a flying edge off Nortje burst through first slip Rassie van der Dussen’s hands and went for four runs.
But two balls later Root ducked into a fast bouncer from Nortje and gloved the ball to wicketkeeper Quinton de Kock.
Nortje again bowled at high pace and was the most threatening of the South African bowlers, while De Kock had another good day behind the stumps, holding five catches.