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"It was an important hour for us," Flintoff told reporters. "We scrapped all day and we needed wickets to get back into this match. I'm reaping all the hard work I've done with (Lancashire physiotherapist) Dave Roberts after my ankle operation."
Flintoff, who got England back into contention at Edgbaston, is playing just his second test in 19 months after an injury nightmare but is proving to be their spearhead in the series.
He finished the day with four for 68, including a hostile spell after tea that accounted for South Africa's top batsman Jacques Kallis.
South Africa closed on 256 for six, having carved out a lead of 25 runs, but another good spell from England's bowlers on Friday morning could limit the tourists' advantage.
The period of play before Flintoff bowled Kallis with a fast and late out-swinger was set up by an lbw appeal that umpire Aleem Dar rejected against the South African, which replays showed should have been out after hitting him on the toe.
An angry Flintoff protested throughout the next over to Dar and his eventual success demonstrated his mood.
"Emotions were running quite high at that point when the appeal got turned down," Flintoff said. "You can chunter as much as you want but you have got to get on with it.
"I have been in to see Aleem and apologised, I shook his hand and we are friends again."
Kallis, who made 64 for his first half-century of the series, said he understood why the dramatic battle he had with a rampaging Flintoff was compared to the one in 1998 when former England opener Mike Atherton faced up to an angry Allan Donald.
"He (Flintoff) bowled a fantastic spell and brought England back into the game," Kallis said. "You get good battles in test cricket and it's good for the game.
"People say test cricket is dying but it's clear that is not the case. What more do you want than periods of play like that?" he added.
Flintoff became only the 10th man to take 200 test wickets and score 3,000 test runs and said it was a statistic he would probably savour in later years. For now, he has more targets.
"It probably doesn't mean that much at this stage but maybe when I'm older I can sit down and look at it more so," he said.
"I want to take a lot more than those stats for the team, and I want to perform better than I have done before and keep improving. At this moment in time I am not driven by stats or records or clubs, I just want to do well."