Pakistan began day two at 4-142 and ended it impressively at 6-310 despite a handful of rain delays cramping both team's rhythm at different stages of the day.
However, Pakistan will play their last Test against Australia in next 3rd January, 2017 at Sydney Cricket Ground, Sydney.
The forecast for the third day is similar to second, wherein only a little over 50 overs were bowled.
Misbah-ul-Haq of Pakistan and Steve Smith of Australia pose with the Commonwealth Bank series trophy during a media session at The Gabba on December 14, 2016 in Brisbane, Australia.
The veteran Pakistan right-hander, however, chose to review and got the call overturned as the ball, that struck a shuffling Younis on the knee roll, seemed to have missed the leg stump.
Steven Smith lead side is leading the test series by 1-0 and will be looking to seal the series when they take on Pakistan for the epic Boxing Day Test match.
However, Australian coach Darren Lehmann said he would disregard the second hit in Brisbane when Maddinson sacrificed his wicket in the hunt for quick runs.
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Azhar's hundred was his 12th in Tests, a brilliant exercise in restraint and patience to keep Australia in the field.
Azhar's secondary brilliance is how indelibly he dispels the exhausted clichés of Pakistani batsmen as zany innovators and impetuous stylists, though you wouldn't call the results effortless.
Most pressure will be on the left-handed Maddinson, who is fighting for his place in the XI after scores of zero, one and four in his first two Tests.
Azhar Ali has been one of the best batsmen in Test cricket in recent times and he was en route to another century at the MCG on Tuesday.
The Pakistani tail resisted Australians extremely well in the second innings of the opening Test, but here, the challenge is to score briskly.
Having previously scored all his centuries on Asian pitches, Azhar's knock at the MCG added to the 139 he scored in Birmingham in August in a losing cause against England.
Paceman Chadd Sayers again also misses out on a Test debut, with Australia sticking with the pace trio of Mitchell Starc, Josh Hazlewood and Jackson Bird.