South Africa closed the opening day of the second Test on 101 for three, a deficit of 102, after they had bowled England out for 203.
But the tourists may have ended the day in a worse position but for a flashpoint involving Flintoff.
Hashim Amla, who made a century in the drawn first Test at Lord's and ended the day here on 18 not out, chipped a Flintoff delivery towards England captain Michael Vaughan, who dived forward at mid-off and claimed a low catch.
Amla started to walk and was nearly off the field when he was told to remain in the middle by 12th man Andre Nel and Proteas coach Mickey Arthur.
Belatedly, the umpires called for a television replay and with the pictures unclear, Amla was allowed to carry on by TV official Richard Kettleborough with South Africa 76 for three.
"It all happened very quickly. Vaughan went up for the catch and the decision went against us," said Flintoff.
"You can't blame Amla for stopping. The decision was made and you have to get on with it."
Arthur added: "I've always been a coach that has advocated technology. If the ball bounces it's not out. I'm 100 percent sure it bounced."
Amla clipped the first ball after the resumption from Flintoff off his legs for four.
Flintoff though thought he had him caught down the legside by wicket-keeper Tim Ambrose for 13 but New Zealand umpire Billy Bowden signalled no-ball.
The all-rounder, appearing in his first Test for 18 months after being ruled out by ankle and side injuries, was at first slip when he caught Neil McKenzie, whose marathon hundred helped draw the first Test at Lord's, off fellow Lancashire quick James Anderson.
Then, coming round the wicket in a move the Proteas feared would pose problems for their left-handed batsmen, Flintoff removed southpaw skipper Graeme Smith, another Lord's centurion, for 44 after the batsman, drawn forward, edged him to first slip Andrew Strauss.
Anderson, who finished the day with figures of two for 39, then bowled the experienced Jacques Kallis of the inside edge for just four.
Shock England debutant Darren Pattinson took the new ball but went wicketless in just the three overs he was given by Vaughan.
Earlier, South Africa fast bowlers Morne Morkel (four for 52) and Dale Steyn (four for 76) did the bulk of the damage after Smith, as he had done in the first Test where England piled up 593 for eight declared, elected to field.
South Africa-born Kevin Pietersen, who made 152 in his first Test innings against the Proteas at Lord's, top-scored with 45 before edging a loose drive off Steyn to first slip Smith.
The Proteas had already had a moment to savour when Vaughan, who made just two at Lord's, edged a beauty from Steyn to Smith and was out for nought.
It was not the way Vaughan, on his Yorkshire home ground, would have wanted to mark his 50th Test as England captain.
Former roof tiler Pattinson, appearing in just his 12th first-class match, replaced fellow Nottinghamshire pace bowler Ryan Sidebottom after the left-arm quick was ruled out with a back strain.
Born in Grimsby, northern England, but raised in Australia, the 29-year-old Pattinson only made his first-class debut, for state side Victoria, in January 2007 after several seasons playing for Melbourne club side Dandenong.
But in six first-class matches for Nottinghamshire this season he has so far taken 29 wickets at 20.86 apiece, figures which persuaded the selectors to pitch him in at Headingley.