Stokes senior was admitted to intensive care in Johannesburg after being taken ill on Monday night but he has responded well enough to treatment for England's vice-captain to commit to the match in Centurion.
Pope would have batted at number six had he been fit to play but his absence opened the door for Jonny Bairstow to return to the side.
Woakes may also have played but with the Warwickshire man quarantined at the team hotel, all-rounder Sam Curran took the field.
England captain Joe Root won the toss and opted to bowl first, perhaps persuaded by a light covering of live grass.
James Anderson was presented with his 150th cap by his former captain Nasser Hussain – the ninth player to reach the landmark in Test cricket, the second Englishman after Sir Alastair Cook and the first specialist fast bowler.