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.
Australia went to stumps on the second day of the pink ball Ashes Test on 378-6, the home side leading England by 44 runs on the first innings with four wickets still remaining.
Will Jacks is set to make his first Test appearance in almost three years after England named their starting XI for the second Ashes encounter against Australia that starts in Brisbane on Thursday.
Pat Cummins is set to miss the second Ashes Test against England in Brisbane after Australia named a squad of 14 for the encounter that did not include the captain.
England captain Ben Stokes has come out and said he will accept criticism for his team's performance in the first Ashes Test but has pushed back at jibes that the tourists are "arrogant".
