The left-hander, who played the most recent of his 14 Tests in January 2022, dominated with 126 from 131 balls behind closed doors at the Junction Oval in Melbourne on Saturday.
Harris top-scored in Victoria's 4-272 as Dylan Brasher also impressed to finish unbeaten on 79.
Pakistan's Babar Azam (left) and Shan Masood go through their paces in the Junction Oval nets. (Joel Carrett/AAP PHOTOS)
The 31-year-old Harris, along with Cameron Bancroft and Matt Renshaw, is vying to take the opening spot Warner will vacate when he retires from Test cricket following the SCG Test against Pakistan in January.
It was Harris's second century of the summer after he belted 164 against Tasmania, also at the Junction Oval, last month.
Pakistan requested another match ahead of the Boxing Day Test after being disappointed when their game against the Prime Minister's XI ended early.
AAP understands the tourists were happy for spectators and media to be inside the ground, but there were problems finding staff for the Cricket Victoria facility at such short notice.
Victoria provided the opposition as Pakistan prepare for the Boxing Day Test in Melbourne. (Joel Carrett/AAP PHOTOS)
Pakistan made 323 after batting first on Friday, with wicketkeeper Mohammad Rizwan staking his claim for a Boxing Day Test recall.
Rizwan hit a free-flowing 50 from 70 balls before retiring during day one of the hit-out.
Saud Shakeel, who has enjoyed a consistent start to his Test career and showed fight against Australia in Perth last week, top scored with 70.
Rizwan was surprisingly overlooked for the first Test, with Pakistan opting for 36-year-old Sarfaraz Ahmed behind the stumps.
Pakistan briefly batted again, making 3-57 before the practice match was brought to an end in the 12th over of their second session in the middle.
The tourists have two more days to fine tune ahead of the start of the Boxing Day Test on Tuesday.
Pakistan went down by 360 runs in Perth - their 15th-straight defeat in Tests in Australia.
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