Skipper Andrew Strauss was dismissed by Morne Morkel with the fourth ball of the day and, as the South Africa seamers threatened to inflict further damage under cloudy skies, it was left to some familiar faces to shift the balance of power.
Jonathan AgnewBBC cricket correspondent
"For South Africa captain Graeme Smith to wait so long to bring Dale Steyn into the attack, he might look back with regret on that decision. He needed to seize the moment because there will be a passage of play in a three-Test series which can decide the overall outcome."
Cook and Trott's disciplined batting at the top of the order has underpinned England's rise to the top of the world rankings - and the watchful pair had to utilise all of their famous powers of patience to defy South Africa.
Proteas captain Graeme Smith, playing his 100th Test, looked to have pulled off a masterstroke when he gave the new ball to Morkel - ahead of the number one ranked bowler in the world, Dale Steyn - and it paid instant dividends with the dismissal of Strauss.
It was the first time in 20 Tests that Steyn had not opened the bowling in the first innings of a match, but, mindful that Morkel had dismissed Strauss six times in eight previous matches, Smith's decision looked inspired.
Morkel struck Strauss in front, but his appeal was turned down by umpire Steve Davis. South Africa referred the decision and were vindicated as replays suggested the ball was going to hit the stumps.
With Vernon Philander causing plenty of problems at the other end, Cook and Trott had to sacrifice flair for fighting spirit to wrestle control.
They were virtually faultless, showing dogged determination to blunt the new-ball attack on an admittedly true surface.
As England's confidence grew, South Africa seemed to run out of ideas, the shift in momentum emphasised when Cook hooked a Steyn bouncer for six on the stroke of lunch.
If the tourists were getting any sort of help from the overhead conditions, it was lost after the interval when the sun came out.
Cook and Trott expertly mixed accumulation with aggression to score almost 100 runs in the session.
Both players brought up their half-centuries, Trott in particular upping the tempo after reaching the landmark.
Only magic or a mistake could separate Cook and Trott - and it proved to be the latter as Trott flashed at a wide one from Morkel to be caught behind by stand-in wicketkeeper AB de Villiers.
The breakthrough brought little respite as Pietersen took advantage of some weary bowlers. Philander, in particular, saw his pace significantly drop late in the day.
Most Test hundreds by an England batsman
Walter Hammond, Colin Cowdrey, Geoffrey Boycott
Ken Barrington, Kevin Pietersen, Graham Gooch, Alastair Cook
Michael Vaughan, David Gower
As Pietersen plundered boundaries, treating the bowling with disdain, Cook quietly moved to the 20th Test century of his career, drawing alongside Ken Barrington, his mentor Graham Gooch, and Pietersen in England's all-time list.
The Essex man had gone 18 innings since his last Test ton - and the calm, assured nature of this innings suggests he will not have to wait as long for his next.
"It was very satisfying," he said of his chanceless knock, off 222 balls. "When you come so close a few times - I think it's been a year since my last Test hundred - it makes it a very special moment.
"It's nice to join Goochie. Clearly he was a great player, and to have the same amount of hundreds as him is special."
Cook never looked like giving his wicket away, but it was a familiar tale of frustration for Pietersen.
After racing towards his fifty, thanks to a range of typically expansive shots, his adventure cost him when he gloved a short ball from Jacques Kallis to De Villiers.
South Africa took the second new ball, but Bell and Cook were equal to the task and will look to increase England's advantage on the second day on a pitch which is already showing signs of turn.
Listen to analysis of the first day's play with Jonathan Agnew and Geoffrey Boycott on
the TMS podcast.
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