Australia captain Ricky Ponting was 61 not out and Michael Clarke 32 not out.
Earlier, Pakistan were bowled out for 258 in reply to Australia's 88, a first innings lead of 170.
Shane Watson took six wickets for 33 runs - the second time in as many matches the medium-pacer had taken career-best figures after his five for 40 in Australia's 150-run first Test victory at Lord's last week.
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