Cook top-scored with 65 to lead the England reply after the tourists tore through the Proteas tail to bowl them out for 291 in the morning session.
But it was no plain sailing as England slumped to 133-5 at one stage, only for Matt Prior to smash a much-needed half-century to guide them to 241-7 at the close.
“It was a tough day’s cricket,” vice-captain Cook admitted. “South Africa bowled well and didn’t let us get away from them and it is definitely going to turn into a scrappy game. They came out here and bowled less bad balls, putting us under some pressure. The game situation is set up nicely for a one-innings game come tomorrow. It is going to be a really good game over the next couple of days.”
England’s hopes of surpassing the South African total now rest with Prior and Graeme Swann (5no) but all eyes are on the behaviour of the seam-friendly Cape Town pitch with the sides so evenly matched.
“We don’t want to be chasing too many but we have seen in recent games that pitches don’t deteriorate as much as you think they will,” Cook added. “We will cross that bridge when we come to it but we will hopefully get a lead with Swanny and Matt tomorrow and put them under some pressure when we bowl.”
For once, Swann wasn’t the England hero with the ball – that accolade went to James Anderson, who saw off tailenders Dale Steyn, Morne Morkel and Freidel de Wet in double-quick time for figures of 5-63 and an eighth Test match five-for.
England’s reply, however, got off to a disastrous start when captain Andrew Strauss edged behind sixth ball and he was soon followed by Jonathan Trott (20), and Kevin Pietersen, who went for a second-ball duck as seamers Morkel and Steyn revelled in the conditions.
Paul Collingwood added 19 before Morkel struck again, then after a battling 60-run stand with Ian Bell, Cook ended his marathon four-hour innings cheaply after finding Ashwell Prince at square leg just after tea.
Bell continued the middle-order resistance with another steady knock before agonisingly falling just two runs short of his half-century, leaving Prior to take over the mantle.