Azhar Ali was run out for 71 in a poor piece of running with Younis, when he could not beat home Mitchell Starc's throw from mid-on to the striker's end.
At tea, after play finally got underway in mid-afternoon following rain, the tourists were 177 for three with Younis on 84 and skipper Misbah-ul-Haq not out 18 to trail Australia's first innings by 361 runs.
Younis drove spinner Nathan Lyon to a diving fielder at short midwicket and hesitated, leading to some indecision with Azhar before Starc swooped in to throw back to the 'keeper standing over the stumps.
In five innings, Azhar has scored 395 runs in this series at 98.75.
He faced 159 balls and looked set in his 227-minute stay before the mix-up that led to his run-out.
Azhar and Younis put on 146 runs for the third wicket, restoring the Pakistan innings after they were six for two.
Azhar had survived a tight leg before wicket review on 59 off Josh Hazlewood with the ball projected to hit the leg-stump, but not enough to overturn Sundaram Ravi's initial decision.
Cricket Australia said Wade was suffering from diarrhoea and nausea. He fell ill in the morning and returned to the team hotel to rest and was expected to recover in time for Friday's play.
Australia have already won the series after victories in the Brisbane and Melbourne Tests, while Pakistan are battling to avoid their 12th straight Test defeat in Australia.
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