Mr Doyle, 64, was in December accused of sexual harassment and indecent assault by two women, including councillor Tessa Sullivan, who quit over the mayor's alleged behaviour.
On Sunday Mr Doyle quit as mayor and as chairman of Melbourne Health after being admitted to hospital, his lawyer Nick Ruskin said.
Mr Doyle is the subject of two investigations, one ordered by the council and another by Victorian Health Minister Jill Hennessy following a third accusation.
A by-election will be held to choose a new Mayor.
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