Australia, who had resumed at 313 for five in their second innings chasing 522 for victory, were bowled out for 406 in the morning session. England won by 115 runs to take a 1-0 lead in the five-match series.
Flintoff will retire from Test cricket after the fifth Test at the Oval next month.
England won their only Test of the 20th century against Australia at Lord's 75 years ago when Yorkshire left-arm spinner Hedley Verity took 15 wickets on a rain-affected pitch, dismissing Don Bradman twice.
Flintoff bowled magnificently for the second day in a row, rapping Brad Haddin on the pads with his third ball which beat the Australian wicketkeeper for pace.
The next drew Haddin forward, caught the outside edge and flew low to Paul Collingwood at second slip. He had not added to his overnight score of 80.
Mitchell Johnson got off the mark with a handsome drive for four off Anderson. He was then struck on the pads by a low full toss from Flintoff which would have hit the stumps but umpire Rudi Koertzen had already signalled a no-ball.
Michael Clarke, 125 not out overnight, unfurled a glorious off-drive to the boundary off Stuart Broad, who had replaced James Anderson at the Nursery end.
Johnson off-drove Broad for four to bring up the 350 but then lost Clarke, who was bowled for 136 by Graeme Swann's second delivery of the morning. The batsman was deceived in the flight by a ball which knocked back his off-stump.
Flintoff, still steaming in from the Pavilion end after more than an hour of high-pace bowling, bowled Nathan Hauritz for one and Peter Siddle for seven.
Johnson, dropped on 36 hitting a difficult return chance to Swann, continued to play his shots while wickets fell at the other end. He was the last man out, bowled by Swann for 63 with nine boundaries.
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