Moeen Ali, on 26 not out, and new batsman Jonny Bairstow, who had scored one, will resume after the break facing a huge task to increase England's 93-run lead to a competitive total as the wicket wears.
England captain Root had to pass a concussion test to be deemed fit to play in the morning after being struck on the helmet by a fierce Mitchell Starc bouncer late on day three.
He battled to reach his 33rd test half-century on a steamy day at the Gabba but was out the next ball, trapped lbw for 51 to leaving the tourists reeling with 10 minutes left until lunch.
England had resumed on 33 for two, with Root on five and Mark Stoneman on 19, and the batsmen survived a tough pace examination before Australia captain Steve Smith turned to offspinner Lyon to break the stand.
Lyon duly obliged, having Stoneman play forward and edge to the Australia skipper, who took a fine lunging catch at slip to remove the batsman for 27.
Not long after, Lyon had England number five Dawid Malan also nick straight to Smith for four.
Moeen survived an early scare with a nick behind off Starc that fell just short of a leaping Smith, who managed to get a finger on the ball before it hit the grass.