Marnus Labuschagne (14) and Steve Smith (two), are the unbeaten batters after the tourists fought back from a diabolical start to the Boxing Day Test.
Spectators were warned via the scoreboards to prepare for severe weather and "seek shelter from exposed areas" as the MCG lights were turned on in the early afternoon.
Marnus Labuschagne clips the ball away on his way to 14 before rain stopped play at the MCG. (Joel Carrett/AAP PHOTOS)
Play started on time on Tuesday morning as the sun shone brightly, but the skies quickly got dark after lunch and players went off the ground.
After a promising start, Khawaja was dismissed for 42 after playing a poor shot off Hasan Ali's (1-21) bowling early in the middle session.
Warner was out for 38 to spinner Agha Salman (1-3) from the final ball before lunch, but not before he and Khawaja made Pakistan pay with a 90-run stand following captain Shan Masood's decision to bowl.
Masood was left deflated when Abdullah Shafique put down Warner at first slip off the last ball of star quick Shaheen Afridi's second over.
Pakistan skipper Shan Masood (r) was frustrated to see David Warner (l) survive an early chance. (Joel Carrett/AAP PHOTOS)
Warner, who smashed 164 in the first Test in Perth, was on two when Shafique dropped a catch that left former Australia coach Justin Langer stunned.
"That's as easy a catch that you'll ever see in Test cricket," Langer said in commentary on the Seven Network.
"I said it before this Test - if Pakistan have got any chance of fighting back in this series, they must field better than they did.Â
"That's an impossible catch to drop. While he'll feel sick about it, it's not acceptable at international level."
Warner's 38 put him on a total of 18,502 runs across all formats, sending him past Steve Waugh (18,496) for the most runs scored by an Australian in international cricket.
Second-placed Warner still has a long way to go before catching Ricky Ponting, who amassed 27,368 runs across his legendary career.
Khawaja had hoped to use images of a dove holding an olive branch, as well as a reference to article one of the Universal Declaration of Human Rights, during the Boxing Day Test to show his support for those suffering during the ongoing conflict in the Middle East.
Instead, Australia's opener walked out to bat on Boxing Day with the names of his children, Aisha and Ayla, written on his shoes.
Usman Khawaja, who had the names of his children inscribed on his right boot, was dismissed for 42. (Joel Carrett/AAP PHOTOS)
The MCG pitch has produced bowler-friendly conditions since the infamous dull drawn Ashes in 2017, which is why Masood chose to bowl first.
"Just having looked at the MCG Tests for the past three years the bowling side has done well," Pakistan's skipper said.
"There's been a bit of weather around so we'd just like to avail every opportunity with the ball."
While Australia went into the match unchanged, the tourists switched three players, including swapping wicketkeepers.
Mohammad Rizwan returned to the side after surprisingly being left out of the XI in Perth as Pakistan opted for veteran Sarfaraz Ahmed behind the stumps.
Fast bowler Khurram Shahzad impressed on debut in Western Australia's capital, but is out injured for the rest of the series.
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