Ms Allan ran for leader of the Victorian Labor Party at a caucus meeting on Wednesday after Daniel Andrews' shock resignation less than 24 hours prior.
The Bendigo East MP will be Victoria's second female leader and the first Labor premier from regional Victoria in almost 100 years.
Public Transport Minister Ben Carroll was chosen as deputy.
Ms Allan entered parliament in 1999 and became the youngest minister in the state's history at 29.
She took over as Mr Andrews' deputy and presumed successor in June 2022 and most recently served as minister for transport infrastructure and the suburban rail loop project.
She was also charged with delivering the now-cancelled 2026 Commonwealth Games until the portfolio was abolished.
Wednesday's caucus meeting started late after Mr Carroll decided to try and throw his hat in the ring for the leadership.
But Ms Allan emerged from the meeting with the numbers to become premier, avoiding the matter going to a vote by membership.
"All positions have been elected unopposed," Box Hill MP and the party's returning officer Paul Hamer told reporters.
"The new premier is Jacinta Allan, the deputy premier is Ben Carroll."
The new ministerial cabinet spot left by Mr Andrews' departure will be filled by Eltham MP Vicki Ward.
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