Paceman Jackson Bird took two wickets, with Josh Hazlewood and Nathan Lyon grabbing one wicket apiece before the premature close at the Melbourne Cricket Ground.
Azhar Ali was unbeaten on 66, with Asad Shafiq on four not out.
Bird bowled Younus Khan for a streaky 21 and grabbed another old-stager in captain Misbah-ul-Haq for 11 in front of a festive Boxing Day crowd.
A warm and muggy morning gave way to a chilly afternoon as a cool change swept through from the west and Pakistan's fortunes took a corresponding dive along with the temperature.
Azhar and Younus had resumed on 60-2 after lunch and carved out a 51-run partnership but it was a stand built on shaky foundations.
Younus was given out lbw for three after Hazlewood hammered into his pad but he mounted a successful review, with the technology showing the ball just missing leg stump.
The 39-year-old survived until the drinks break but was out shuffling across his crease and hanging out his bat against Bird, who bowled him through the gate.
Misbah clubbed Lyon for six over the long on boundary on the first ball faced against the spinner but lasted only a couple of more overs before Nic Maddinson dived low and forward to clutch a one-handed catch at short leg off Bird's bowling.
Umpires called for a video review but the footage showed the fielder had just got his fingers under the ball above the grass.
Azhar rode his luck to edge Bird through gully and the slips cordon for four before rain halted play and brought an early tea.
Paceman Hazlewood earlier dismissed number three batsman Babar Azam for 23 on the last ball before lunch with captain Steve Smith taking a fine, low catch in the slips.
Lyon dismissed opener Sami Aslam for nine just before the drinks break of the first session after Pakistan captain Misbah won the toss and elected to bat.
Brought on in the 12th over, the offspinner had Sami caught behind with his third ball, a venomous turning delivery that reared off the pitch and clipped the batsman's glove on the way through to Smith at slip.
Australia won the first test by 39 runs in Brisbane and brought an unchanged side to the MCG where they will bid to seal the three-match series with a game to spare.
Pakistan, who have lost four tests in succession, made one change, with right-arm paceman Sohail Khan replacing left-armer Rahat Ali.
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