Opener Sami Aslam and one-down Babar Azam were sent back to the pavillion by the Kangaroos before day's end.
Aslam was caught by Matt Renshaw off Mitchell Starc, while Babar was caught at first slip by captain Steven Smith off Nathan Lyon.
Earlier, Australia, riding on the back of 111-run partnership between Usman Khwaja (74) and Smith (63), stretched their first innings lead to 489 before declaring their innings.
Pakistan now have two days left to save the day-night Test by chasing a historic target.
At dinner
Australia were helped by Usman Khwaja (74) and captain Steven Smith's (63) partnership of 111 runs as the hosts set a daunting 490-run target for Pakistan to chase with two days and one session left in the first day-night Test at Gabba.
Pakistan managed to score 142 in reply to Australia's first innings total of 429 courtesy Sarfraz Ahmed's unbeaten 59, however, their bowlers, in the second innings, were again unable to restrict the hosts.
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At dinner, Peter Handscomb (35) and Matthew Wade (one) were unbeaten when Australia declared their innings on 202-5.
For Pakistan, Rahat Ali was the most successful bowler with two wickets from his 10 overs for 40 runs.
Leggie Yasir Shah and left-arm pacer Wahab Riaz and Mohammad Amir bagged one wicket each.
At tea
Australia built their lead to 327 runs with eight wickets in hand at tea on day three of the first day-night test in Brisbane on Saturday after bowling Pakistan out for 142.
Pakistan's first innings total was 88 runs short of the 230 required to avoid the follow-on but captain Steve Smith elected not to enforce it and put his team in to bat the touring side out of the game.
Pakistan's pacemen took two early wickets, but captain Smith (eight not out) and Usman Khawaja (13) survived to tea, with Australia on 40 for two. Opener David Warner was out for a free-swinging 12, skying a pull shot off Mohammad Amir for an easy catch at mid-on for Wahab Riaz.
Rahat Ali grabbed his first wicket of the match when he had opener Matt Renshaw edge to Younus Khan for six in the slips. Pakistan lost an early review for caught behind on Smith on his first ball and the Australian skipper smashed a boundary on his next.
Day two: Pakistan 97-8 in reply to Australia 429 at stumps
Routed by Australia's seamers late on day two, Pakistan resumed in the afternoon on 97-8, and wicketkeeper Sarfraz Ahmed and Mohammad Amir built a plucky 54-run partnership before paceman Jackson Bird struck to remove Amir for 21.
The caught behind appeal was turned down by umpire Richard Illingworth but Smith successfully reviewed it and the technology showed the paceman had feathered an inside edge through to wicketkeeper Matthew Wade.
Rahat was run out for four with a piece of typical fielding brilliance from Warner to wrap up the innings. Television replays showed he had not grounded his bat when returning to his crease after an aborted single. Sarfraz was left unbeaten on 59.
Pakistan all out for 142 in reply to Australia's 429
Pakistan were bowled out for 142 in their first innings before tea on day three of the first day-night test against Australia in Brisbane on Saturday, conceding a first-innings lead of 287 runs. The hosts decided not to enforce the follow-on and will try to bat Pakistan out of the game.
Wicketkeeper Sarfraz Ahmed and Mohammad Amir resumed with Pakistan on 97-8 and built a plucky 54-run partnership before paceman Jackson Bird struck to remove Amir for 21.
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The caught behind appeal was turned down by umpire Richard Illingworth but captain Steve Smith successfully reviewed it and the technology showed the paceman had feathered an inside edge through to wicketkeeper Matthew Wade.
Rahat Ali was run out for four to wrap up the innings, dismissed after television replays showed he had not grounded his bat when returning to his crease. Sarfraz was left unbeaten on 59
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