After Philander made light work of the Sri Lankan tail, Cook and Elgar put on yet another 100 run partnership, their second in the match, to put the hapless Lankans on the back foot. Amla then came in and played some fancy shots despite not looking anywhere near his best.
Three quick wickets, two from de Silva, did not hamper South Africa's progress as de Kock entered declaration mode and skipper du Plessis played with a solidity and confidence that can only stem from a 300+ lead going into the final innings on a green surface.
Lanka, meanwhile, will rue the fact that they did not get closer to the South African total earlier. Cook went on to make his third Test hundred, underlining the importance of grit and patience in Test cricket.
Here are the talking points from Day 3 at Port Elizabeth.
#5 Philander puts an end to all speculation in the very first over
Vernon Philander is a real beast of a bowler anywhere in the world. In South Africa, on a green surface, he is a monster. Sri Lanka had got an early taste of the Philander medicine when he reduced them to 61/4. But de Silva's patient knock on Day 2 made them hopeful that they could come near the Proteas total.
Any such thoughts were soon thrown to the wind as Philander produced the perfect seam bowler's delivery in the very first ball on Day 3. The hint of away movement squared up de Silva, who promptly edged to de Kock's mitts to end Lanka's hopes.
Philander wasn't done though and dismissed Lakmal as well in the last ball of the first over of the day to complete yet another five-wicket haul at home, his 11th one overall.
#4 Cook and Elgar match 87-year-old record
Stephen Cook and Dean Elgar are not the prettiest of openers. But in a country which has produced openers like Graeme Smith, Gary Kirsten and Andrew Hudson in the ugly-but-beautiful mould, Cook and Elgar are heavenly, if not flamboyant.
The duo had no 50+ stand in 8 innings together at the top before this Test. All of a sudden they have two in a single match, becoming just the second South African opening pair to make two hundred-run partnerships in the same Test. The previous one came in 1929.
Cook went on to notch up a fine hundred while Elgar was dismissed soon after his half-century. With South Africa leading by 81 runs going into their second innings, it was important that they did not lose early wickets in overcast conditions. The openers not only negotiated the seam movement but also set a firm platform for the middle order to cash in on.
#3 Elgar flatters to deceive
Elgar has arguably been South Africa's best opener in Tests since the retirement of Graeme Smith. He, in every way, looks like he has modelled his game on the former Proteas skipper. Despite standing way shorter than Smith, Elgar has shown the same staunch determination and perseverance as Smith.
His hundred in Sri Lanka in 2014 showed that he was ready for a battle in any conditions. In Australia, against a strong Aussie bowling attack, he showed calmness and understanding to notch up another Test ton.
But there is something about Elgar that isn't Smith-like. The former opener was a master at converting his starts into hundreds, if not double hundreds. He wasn't one to walk away in the midst of a battle. Elgar, meanwhile, has given his wicket away far too often after looking set for a big score.
#2 Stephen Cook and his confusing technique
Stephen Cook and Elgar are similar in the way they both overcome their technical deficiencies with defiance. Cook was criticised to no end in Australia for his tendency to hang out his bat against the swinging ball.
So uncertain was he in his foot movements and judgement that Starc toyed with him in the first two Tests. There were immediate calls to drop the opener and they were warranted since his initial movement of going back into the crease and bending down to meet the ball displayed what looked like fear against sheer pace.
If Australia thought so, they were horribly mistaken as Cook brought out his domestic form at Adelaide in the day-night Test to compile a fine hundred. As if that was not enough to mute his attackers, he made yet another one here in PE against Lanka in the second innings when the ball was moving around under cloud cover and heavy winds.
#1 Pakistan's Brisbane chase in Protea minds
South Africa had stamped their authority in the game already and had a mighty lead of 358 when Quinton de Kock walked to the middle. On a green surface, with bowlers of the quality of Philander, Abbott and Rabada, against a questionable, adventurous Lankan batting line-up, the lead should have been enough to prompt a declaration.
With rain threatening quite a few times during the day and lightning causing an early lunch, a du Plessis declaration would not have come as a surprise, especially after his controversial declaration at Adelaide.
But Pakistan's recent heart-in-the-mouth chase of 490 against Australia in Brisbane seemed to be on South African minds as de Kock and du Plessis showed intent but never looked like declaring. Even with the lead closing in on 450, a declaration looked like the last thing on du Plessis' mind as he walked off at stumps on Day 3.
Looking for fast live cricket scores? Download CricRocket and get fast score updates, top-notch commentary in-depth match stats & much more! 🚀☄️