Australia's Warner out for 34 in farewell Test as rain thwarts Pakistan
Marnus Labuschagne was on 23 and Steve Smith six in their team's 116 for two before play was ended by bad light and rain before tea.
The hosts trailed by 197 runs on a day where Warner was denied a crack at a cherished century in his 112th and final Test match.
Warner was dismissed for 34 and looked annoyed as he left the Sydney Cricket Ground to a standing ovation from his home crowd.
The 37-year-old opener, known throughout cricket as 'the Bull', was beaten by the extra bounce and turn out of the rough by offspinner Agha Salman.
He edged a catch off the shoulder of his bat to a delighted Babar Azam at slip.
Warner, who still has a potential second innings to bat in his last Test, has now scored 8,729 Test runs since his 2011 debut at an average of 44.53 with 26 centuries.
He had a reprieve when he was put down on 20 by young debutant Saim Ayub at first slip in Aamer Jamal's first over.
It continued a wretched time for Pakistan in the field in this series with a number of dropped chances.
Ayub put his head down in anguish after fluffing the simple chance, which came after his two-ball duck in Wednesday's first innings of his first Test match.
Khawaja, who averages 130 in Tests at the SCG, fell to a gloved catch down the leg-side off Jamal for 47, that was detected on review after a patient 143 balls at the crease.
Australia still have a strong batting lineup to come with Smith averaging 72 in 11 Tests at the famous SCG and Labuschagne 76 at the ground.
Travis Head and Mitchell Marsh, who already has scores of 90, 63 not out and 96 in this series, will be next in.
The rain interruption continued the Sydney Test's soggy weather reputation. The SCG has suffered 26 washed-out days, the most of any Australian Test ground.
Australia clinched the three-match series with a tense 79-run win in the second Test in Melbourne over Christmas.
