Susan Aitken, the opposition SNP's social work spokeswoman, had been favourite to take over from Graeme Hendry, who stepped down for family reasons after two years in the post. She defeated west end councillor Kenny McLean for the post.
However, her election by a convincing majority of the city's 27 SNP councillors has been overshadowed by the continuation as deputy of Councillor Billy McAllister.
He was re-elected unopposed, despite being convicted last week at Glasgow Sheriff Court of acting in a threatening or abusive manner. He was fined for shouting and swearing at a man who classes himself as disabled at a 'bedroom tax' meeting.
It prompted calls from Shadow Scottish Secretary and Labour Glasgow East MP Margaret Curran for the SNP to take action against Mr McAllister, who has been deputy to the last four SNP group leaders on the council.
Ms Aitken, 42, has worked for Age Concern Scotland, at Holyrood for MSP Christina McKelvie and, on a temporary basis, for the SNP parliamentary group central office.
Ms Aitken had been given the party's lead role on social work in May 2012 and an SNP spokesman said she had "successfully held Labour to account over issues such as its decision to close learning disability day centres, introduce charging for community alarms without consultation and, most recently, questioning the need to introduce charging for elderly day care services".
The councillor said: "I am hugely honoured to have been chosen as the new leader of the opposition.
"I know there is a great deal to do over the coming months and years. Labour's leadership in Glasgow is tired. Scratch the surface and there is little vision for our great city.
"I will be arguing strongly that only the powers of independence will provide the opportunities to improve the lives of Glaswegians and the economy of our city."