South Africa made 441 in their first innings and had reduced England to 95 for four in reply at close of play.
Left-hander Graham Thorpe, was on six, and nightwatchman Matthew Hoggard had yet to face a ball.
"The plan was obviously not to lose four wickets tonight but the rest of us will have to bat well," Flintoff said.
"We are going to have to scrap, but we have been in this position before in the past 12 months and there is a great deal of confidence among the team that we can get back into the Test.
"Over the past 12 to 18 months we have improved as a side and it seems that every time we need a performance from someone, somebody sticks their hand up and puts a special one in. Tomorrow will be no different," added the fast bowler, who took four wickets for 79 runs for England.
South Africa's Jacques Kallis scored 149 -- his 19th Test century -- and shared a 104-run eighth-wicket partnership with Nicky Boje (76) to steer the home side to a competitive total.
During the second test in Durban last week South Africa bowled England out for 139 in the first innings but allowed the visitors to score 570 for seven in the second innings.
Kallis said that South Africa were not perturbed by that and felt they could capitalise on their strong position at Newlands.
"We know what we have to do, which is to try and knock over the nightwatchman early tomorrow and then have a go at Flintoff with a little bit of juice in the wicket to assist us," Kallis said.
"There is enough in this wicket to make sure that if we land the ball in the right area consistently it will make batting tough.
"I don't think the guys will have any doubts. We are confident in what we have to do."
