In her first parliamentary act in the top job, Ms Allan on Tuesday presented the lower house speaker Maree Edwards with details of her new ministry to the delight of Labor members.
Mr Pesutto also informed the house of changes to his shadow cabinet, before he and Ms Allan exchanged a handshake across the table.
The pair are set to go head-to-head during question time on Tuesday afternoon.
Nicole Werner was also sworn in as the newest member of parliament after winning the Warrandyte by-election following the retirement of Liberal stalwart Ryan Smith.
She received a standing ovation and hugs from Liberal and National MPs in the chamber.
Ms Allan's first cabinet was sworn in at Government House on Monday after the sudden retirement of Mr Andrews last week.
The Bendigo East MP ceded her high-profile roles as minister for transport infrastructure and the Suburban Rail Loop to Assistant Treasurer Danny Pearson as part of the cabinet reshuffle.
Newly appointed Deputy Premier Ben Carroll has become minister for education and medical research.
Tim Pallas, who vied for the deputy premier role, remains treasurer after speculation he could follow Mr Andrews out the door.
Mr Pesutto also revealed his new shadow ministry on Monday, prompted by Matthew Bach stepping down from cabinet to take a teaching role in the UK.
Under a raft of changes, former opposition leader Matthew Guy returned to the frontbench as public transport spokesman after leading the coalition to a second election drubbing in November.
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