Siddle dismissed Imran Farhat (38) and Khurram Manzoor (0) in the space of four balls after the openers had put on 63 runs for first wicket.
Pakistan's cause was also not helped by two run-outs -- those of Mohammad Yousuf (7) and Umar Akmal (8).
Salman Butt was unbeaten on 34 with Shoaib Malik, on 4.
The tourists need another 226 runs to avoid the follow-on.
Earlier, riding high on a double century from skipper Ricky Ponting, Australia amassed 519-8, before declaring their first innings just before the tea break.
Ponting, continued from where he left off on Thursday and was in hitting mode as he went for runs right from the onset.
Dropped by Mohammad Aamer on zero, he went on to score a massive 209, his third-highest Test score, and his best on his home ground. Ironically, it was Aamer though who went on to dismiss him, caught by Mohammad Yousuf at extra cover.
Pakistan could have dismissed Ponting earlier, but Imran Farhat dropped him at cover when he was on 167.
Michael Clarke, who joined the captain in the run fest, hit a career-best 166, eclipsing his 151 on Test debut against India.
Brad Haddin (41), Marcus North (21) and Mitchell Johnson (9) hit some lusty blows before Australia declared the innings.
For Pakistan, who trail 0-2 in the series, leg-spinner Danish Kaneria finished with 3-189 from 42.5 overs, while Aamer and Mohammad Asif picked two wickets apiece.
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