Bairstow could not finish the task, though, becoming the first England Test batsman to get out lbw a run short of a century since Eddie Paynter against Australia at Lord's in 1938.
In view of England's fluctuating Test form, the need for consistency among the bowlers has been a topic of conversation in the England group.
Cook's opening partner, Keaton Jennings, has been under pressure after failing to make 50 in six previous innings and he was unable to build any foundations again after another brief spell at the crease.
But as they try to hit back and earn a 2-2 series draw in the final match of four in Manchester, they may again have to take a last-minute gamble on the well-being of Philander - who has this time succumbed to an untimely back spasm.
The James Anderson End was formally christened before play but any prospect of the home favourite immediately bowling from it disappeared when Root opted to bat first.
Never mind the psychological tiredness, South Africa also seem to be carrying numerous physical injuries too; beside Vernon Philander and Chris Morris who are missing this match, it was noticeable on Saturday morning how Maharaj and Heino Kuhn were limping when they had to chase the ball.
With 109 runs in seven innings, his prospects of reaching this month's West Indies series look increasingly slim.
Having made a strong impression on debut at the Kia Oval, he nearly played on with a single to his name, slashed wildly over the cordon on 15 and was roundly beaten by Keshav Maharaj just before lunch.
With his End, the crowd and half of Lancashire seemingly behind him, Anderson needed just three balls to nail South African opener Dean Elgar. Cranking himself up to full pace and ferocity, he burst a lifting delivery off the edge and into the outstretched right mitt of de Kock.
Root and Ben Stokes (58) struck three boundaries combined in the 59th over to gather some momentum with the England captain crossing 5,000 runs in Test cricket, few overs later.
England's erratic dominance continued straight after the evening drinks break, when Keshav Maharaj, on 1, edged Moeen off the tip of Bairstow's gloves and away through his legs to safety.
Morkel will resume on 18 not out on the third day. Having nearly nicked Morkel behind, the captain then followed the bad example set by his departed team-mates in offering a thick edge of his own, only for De Kock to inexplicably fail to dive.
Belief that Bairstow could actually get to three figures was sacked by two extraordinary shots that saw him move from 80 to 90 in the 106th over of the innings, bowled by Duanne Olivier. Getting the wicket, KG (Rabada) bowling Stokes, that puts us in a good position.