England face an uphill battle to save the first Test after another chastening day at The Gabba.
Bowled out for 147 on a curtailed opening day, England paid the price for missing a host of chances on Day 2 as Australia reached stumps on 343 for seven.
It left England trailing by 196 runs and facing the very real possibility of an innings defeat.
England simply couldn't deal with David Warner and Travis Head, with the latter picking up a rapid-fire century, while Warner opened his series with a streaky 94.
Warner had three let-offs along the way. He was clean bowled by an overstepping Stokes on 17, was let off by Rory Burns in the slips on 48 and survived a close-range run out on 60 - Haseeb Hameed missed the target from a couple of yards.
Warner was eventually taken out by Ollie Robinson, who impressed throughout the day, taking three for 48. But, Head was on hand to hammer home the advantage with 112 not out. His 85-ball century was the third fastest in series history.
Head managed to bat on even after being struck in the forearm by Mark Wood early in his innings and was pinned by a wayward beamer just before the close.
Jack Leach was victim to 95 runs in 11 overs, leaving England fans scratching their heads over the decision to leave out record-breaking seam duo James Anderson and Stuart Broad.
Stokes' flawed footwork still rankled too, with the revelation that his would-be 'dismissal' of Warner was one of 14 no-balls he sent down in the morning session, none of which were called in real time. It was later revealed that the technology supposed to monitor the front foot had malfunctioned and was not being used by the third umpire.
With the new ball, England needed an immediate impact, and Robinson gave them one. For his first Ashes outing, he bowled superbly, and was into his third over when he nipped one away and had Marcus Harris nicking low to Dawid Malan at third slip.
It briefly looked like more could follow, with Wood hitting 94mph in his first over and causing Warner some clear discomfort. Stokes, returning here after a five-month break, also had a lively start.
His second ball sailed agonisingly wide of Malan off Warner's edge and his fourth snaked through the defences to clip the top of off stump. Stokes' muted celebrations hinted at what would follow - Warner was recalled to the crease after replays showed Stokes' boot clearing the whitewash.
It turns out that was as close as England would get to a second wicket before lunch, with Marnus Labuschagne leaving intelligently and punishing the bad balls as they crept in while Warner scrapped his way into the game.
A competitive battle shifted dramatically in Australia's favour when Leach entered the attack. His first three overs shipped 31, including two towering sixes from Warner and one from Labuschagne.
The latter reached 50 just before lunch but Warner should never have followed him to the landmark, nicking Robinson's fourth ball of the straight to slip only for Burns to fumble the chance. Having been dismissed by the first ball of the series, this was another moment to forget.
Warner kept offering opportunities, but England were unable to capitalise and allowed him to score at a good rate. He even fell flat on his face, dropped his bat and gave Hameed a golden chance to take his stumps. In line with England's general performance, he missed the target.
For a short period England rallied, Labuschagne (74) carving Leach to point to end a draining stand of 156 and long-time nemesis Steve Smith banking a rare failure when he was caught behind for 12.
Robinson then took two in two balls - Warner's patchy but priceless knock ending with a miscue to Stokes at mid-off before Cameron Green offered no shot to a big inswinger and lost his off stump.
Chris Woakes chipped in with the wicket of debutant Alex Carey but Head was again scoring well. He looked vulnerable early on but even when times were hard England failed to get the job over the line.
He took advantage against a visibly struggling Stokes, cracked Root over the ropes when he entered the fray and continued the uncomfortable theme of bullying Leach with fours and sixes. One shot away from a century he middled Chris Woakes down the ground, celebrating his third Test ton with fitting emotion.
Root had opposite number Pat Cummins caught at leg-slip and Head was floored by Wood's accidental beamer, but Australia had already done enough to assume a strong position at The Gabba.