Lancastrian bowler dropped into the off-side off Makhaya Ntini and called for one - he actually got five as Dale Steyn's throw, which would have dismissed him had it been a direct hit, missed the stumps and raced to the ropes.
However, Anderson's working over contributed to his departure for a Test-best 34 when Steyn followed up with a full one, and when Kevin Pietersen perished in the next over, South Africa's grip strengthened.
It was Jacques Kallis who halted Pietersen's mini-counter with one that attracted a nibble outside off-stump and the same bowler eventually sent back Cook, who squirted a full delivery high to short cover, having dedicated 60 overs to his 60.
In between, Ian Bell climbed into a cut at the lanky Morkel, only to be brilliantly caught - one-handed diving away to his right - by AB de Villiers in the gully.
Any further delay to England's defeat - following a debilitating deficit of 319 - appeared to firmly rest with Flintoff and wicketkeeper Tim Ambrose.
Flintoff, playing his first Test for 18 months and wearing one of Chris Tremlett's larger shirts in preference to his own for comfort, arrived at the crease with England 6-152.
He and Ambrose, who spent 40 minutes on nought, combined in a determined rearguard.
Their partnership had just begun to flourish in fact when Steyn profited from Ambrose's loose cut in the seventh over with the new ball.
It was the Flintoff of old for the next quarter of an hour as he boomed fours off the front foot.
But the sweetest striking was that of Broad who, unflustered by the loss of No.10 Monty Panesar to Steyn, pierced the field on both sides of the wicket to reach his third Test half-century this summer off 41 balls.
His latest effort took his fledgling career average to 41, the same as top-order players Vaughan and Andrew Strauss, and allowed Pattinson some glory of his own - the first of two heaves over mid-on for four off Harris putting England briefly in credit.
But any hope of taking the match into a final day went moments later when Australian-raised Pattinson had his stumps rearranged - and the Proteas openers ended proceedings.
England 1st Innings 203
South Africa 1st Innings 522
England 2nd Innings
Strauss c Boucher b Ntini 0
Cook c Amla b Kallis 60
Vaughan c Boucher b Ntini 21
Anderson lbw b Steyn 34
Pietersen cBoucher b Kallis 13
Bell c de Villiers b Morkel 4
Ambrose Boucher b Steyn 36
Flintoff c Kallis b Morkel 38
Broad not out 67
Panesar b Steyn 10
Pattinson b Morkel 13
Extras 31 (b 4, lb 11, w 2, nb 14)
Total 327 (all out; 107 overs)
FoW: 1-3, 2-50, 3-109, 4-123, 5-140, 6-152, 7-220, 8-238, 9-266, 10-327
Bowling
Steyn 28-7-97-3 (1nb)
Ntini 25-7-69-2 (5nb, 1w)
Morkel 22-4-61-3 (8nb, 1w)
Kallis 17-3-50-2
Harris 15-5-35-0
South Africa 2nd Innings
Smith not out 3
McKenzie not out 6
Extras 0
Total 9 (0 wickets; 1.1 overs)
Bowling
Broad 1-0-8-0
Pattinson 0.1-0-1-0