Unite has refused to nominate either candidate in the Labour deputy leadership race after two of the other biggest unions backed Bridget Phillipson.
GMB and Unison both said they are backing the education secretary following meetings with their leaders on Thursday.
They are throwing their support behind Ms Phillipson over the only other candidate, Lucy Powell, who recently lost her job as leader of the House of Commons during the cabinet reshuffle.
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However, Unite, which has more than 1.2m members across different industries, said neither candidate represents the change required in the Labour Party and said workers and communities “have had enough”.
In a blow for both candidates, Unite general secretary Sharon Graham said: “Britain needs change, not more of the same. Workers are leaving Labour in droves and tinkering will not stem the tide. Unfortunately, this election does not offer the alternative that Britain needs. For everyday people, it is irrelevant.
“Labour must deliver real change. We need huge investment into our crumbling infrastructure and our public services, a pay rise for British workers and end to the private profiteering that helps drive inflation.
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“Until the government makes different choices, they will continue to haemorrhage support.”
Ms Phillipson had already been nominated by three other trade unions – Community, the National Union of Mineworkers and Usdaw – to replace Angela Rayner after she resigned from government over her tax affairs.
The education secretary has been put forward as Number 10’s candidate.
Ms Powell has been backed by one union, so far.
The Fire Brigades Union (FBU), which has nearly 34,000 members, said it was supporting her call to scrap the two child benefit cap and for full delivery of the Employment Rights Bill.
FBU general secretary Steve Wright said if Ms Powell won it would “send a clear message that the leadership must change direction”.
Unison represents 1.3 million public services members while GMB has more than 560,000 members from across the workforce.
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Linda Hobson, chairwoman of Unison’s Labour Link committee, said Ms Phillipson will be a “strong, persuasive and passionate voice” to “help steer the change that people voted for”.
“She has a clear understanding of unions and will be a powerful voice for Unison members working across public services.”
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Gary Smith, GMB general secretary, said the union was “proud” Ms Phillipson has been a member for 20 years.
He said the GMB looks forward to Ms Phillipson “delivering on Labour’s promise” to reinstate the School Support Staff Negotiating Body, aimed at aiding support staff.
On GMB’s support, Ms Phillipson said: “It is humbling to receive the nomination of my own trade union, GMB, for the deputy leadership of the Labour Party.
“The GMB is a powerful voice for working people and their values in every corner of our country and I am deeply proud to be their choice for deputy leader of our party.
“My campaign is getting support from every part of our movement. I will be a deputy leader for every part of our country at cabinet, uniting the party, telling Labour’s story, and bringing the change the British people want to see.”
The two unions’ support of Ms Phillipson came the day after she said she had been the victim of “sexist briefings” – notably rumours, later proved false, she would be sacked from her cabinet role during the recent reshuffle.
“I’ve been underestimated most of my life,” she told the BBC and said she found it amusing she is being touted as Number 10’s preferred candidate after that.
