At lunch on the second day, England were 221 for seven.
That left them 85 runs in front after they had dismissed Australia for just 136, with James Anderson taking an Ashes-best six for 47, yesterday.
Moeen Ali was 23 not out and Stuart Broad 10 not out at lunch, with the five-match series all square at 1-1.
England resumed on 133 for three, with Joe Root 30 not out and Jonny Bairstow unbeaten on one.
But next over Johnson got Australia right back into the match with two wickets for no runs in three balls.
Bairstow had been recalled after England dropped his Yorkshire team-mate Gary Ballance following Australia's mammoth 405-run win in the second Test at Lord's,
But despite averaging over 100 for county champions Yorkshire this season, Bairstow exited for just five as he gloved a brute of a rising ball from Johnson to wicket-keeper Peter Nevill.
It was a fitting way for spearhead quick Johnson to become the fifth Australian after Dennis Lillee, Shane Warne, Glenn McGrath and Brett Lee, to take 300 Test wickets
Root, who made a hundred in England's 169-run win in the first Test in Cardiff, regained the initiative with a flurry of fours.
His pull off left-arm fast bowler Mitchell Starc saw Root to a 49-ball fifty.
England had seen Ian Bell (53) give his wicket away against off-spinner Nathan Lyon yesterday and Root was also responsible for his own downfall on 63.
Root chased a wide ball from Starc and edged straight to Adam Voges at first slip.
England were in even greater danger of not capitalising on their excellent first day when Jos Buttler was lbw for seven to Lyon to leave them 190 for seven.
Lyon, bowling in short spells, had now taken three for three in 14 balls on a pitch providing increasingly sharp turn. But Ali broke the shackles by cover-driving Starc for four.
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