Resuming on 378-6, Alex Carey made his way to 63 while the other overnight batter Michael Neser scored 16.
After dismissing both players, England were frustrated when Mitchell Starc and Scott Boland combined for partnership of 75 for the ninth wicket.
Starc was the more dominant of the duo and hit a valuable 77 while Boland just hung in for 21 not out, but soaked up 72 balls.
Brendan Doggett also contributed 13 as Australia went past the 500-mark to eventually be bowled out for 511, and take a lead of 177 on the first innings.
England now had the task of batting with the lights in full effect and lost Ben Duckett for 15 while Ollie Pope made 26.
Zak Crawley looked in decent form but the opener was caught by Neser off his own bowling to walk to teh dressing room for 44.
First innings centurion Joe Root could manage 15 before Starc had the England kingpin dismissed for 15 to leave the tourists on 121-4.
It was disastrous end to the day for the visitors when Harry Brook was caught behind off Boland.
England finished on 134-6, still trailing by 43 runs, with Ben Stokes and Will Jacks having a massive task on day four if they want to rescue the game.
There was controversy following the first day of the third Ashes Test in Adelaide when the supplier of the 'Snicko' technology admitted an error after Australia's Alex Carey suggested he was out caught behind.
Australia captain Pat Cummins will feature for the first time in the Ashes after being included for the third Test in Adelaide, while spinner Nathan Lyon also returns to the XI.
England have confirmed one change to their XI for the must-win third Ashes Test, starting in Adelaide on Wednesday, with Josh Tongue replacing fellow fast bowler Gus Atkinson.
Australia batter Usman Khawaja says he is over his back injury and "ready to go" ahead of the third Ashes Test against England that starts in Adelaide in 17 December.
