Councillors supported the nomination of Margaret Smith after deciding that it would be inappropriate for Richard Lewis, the previous nominee, to be elected lord mayor later this month.
Mr Lewis has been reported to the ombudsman by all five political groups of Swansea Council.
It is also alleged that Cllr Lewis abused his position as Deputy Lord Mayor and prospective lord mayor during the current council election campaign.
The ombudsman will decide whether the complaint should be investigated.
A joint statement from the five political groups said: 'We believe it would be inappropriate for councillor Lewis to be elected lord mayor of Swansea while he is the subject of a complaint to the ombudsman.
'These are very serious allegations which touch directly upon the nature of the office of lord mayor, and it is only fair to all concerned that councillor Lewis is not elected lord mayor at this time.
'We have jointly taken this decision at this time, having sought legal advice and being mindful of the need to act before the inauguration.
'The office of lord mayor of Swansea is a great honour to the city and one which must maintain the highest standards of integrity at all times.
'Councillor Margaret Smith has been nominated lord mayor. We fully endorse her nomination and offer her our full support during her year in office.
'The decision taken today by the council in no way prejudices the ombudsman's deliberations.
'If councillor Lewis is cleared of the complaints there may be an opportunity in the future for him to be nominated as lord mayor.'
The inauguration of Mrs Smith as lord mayor of Swansea will take place in July.
Mrs Smith, an independent councillor for Pennard, said: 'I am greatly honoured to be nominated as lord mayor of Swansea.
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