Councillors agreed the proposal to shut St Raymond's Primary, Castlemilk.
It had been proposed the children would move into units within three mainstream schools across the city. However, councillors agreed pupils will now have the option of attending another Additional Support for Learning school.
Parents had argued that their children, many of whom have autism, would not cope with being integrated with other pupils and called on the plans to be rejected.
Jean McFaddden, executive member for education, had said the move was part of the council's policy to achieve more integration of special-needs children into mainstream education.
The Evening Times reported this week that parents and a local MSP were urging councillors to reconsider the plans and allow the school to stay open.
The recommendation to close the school was approved with the backing of the SNP opposition members.
Moira Branston, whose sons Dylan, 11, and Ben, 9, attend St Raymond's, said she was angry but not surprised by the decision, which will affect about 30 youngsters.
She said: "Dylan is going to secondary, but I don't know which school Ben will be going to and school breaks up today.
"He will not be going to a mainstream school. I put in a placing request for another special needs school months ago and am still waiting.
"This is disrupting for the children, who are expected to go back in August and get settled in again. Then, in October, the school will shut and they have to start all over again somewhere new.
"That is not putting the child's interests first. All it will do is mess them up and confuse the children."
A council spokeswoman said: "It was agreed no pupils will have to go to a unit within the mainstream schools and will have the option of attending another Additional Support for Learning school."
James Dornan, SNP MSP for Cathcart, had backed the parents in their fight.
He said: "This is a decision that I, parents, children and many of my constituents think is wrong and not necessarily in the best interests of the children.
"I support moves towards mainstreaming, but the council has allowed monetary decisions to cloud their judgement.
"I intend to write to the Education Secretary Mike Russell asking for this decision to be called in by the Scottish Government."