Glasgow City Council officials recommended that St Oswald's school, in Cathcart, should shut, and members voted for this in December, despite overwhelming opposition from parents.
Pupils will now be relocated to a new wing of St Margaret Mary's mainstream secondary school, in Castlemilk, by August.
Parents, who have been lobbying against the closure since plans were revealed last year, were given a glimmer of hope by education bosses who informed them that the matter was to be referred to the Scottish Government under legal guidelines.
They launched a petition for education minister Mike Russell which gathered more than 240 signatures in just days.
But the Scottish Government told the Evening Times yesterday that as the St Oswald's plans are classed as a 'relocation', there is no scope for them to step in.
This news came on the same day that parents received a letter wrongly informing that the decision WOULD be referred to ministers under the Schools (Consultation) (Scotland) Act 2010. The letter, signed by education director Maureen McKenna, invited them to submit their views to the Scottish Government.
A spokeswoman for Glasgow City Council said that a letter clarifying the situation will be issued on Monday.
Concerned mum-of-four Alison Neil, who has two children at St Oswald's, said: "This is a shambles.
"The council told us we could appeal to the Scottish Government so this is what we did.
"Now we learn that this is not the case. But I can assure you we will not stop fighting this."
Alison, 36, who has three children who suffer from autism, said she still plans to deliver the petition to the education minister.
The decision to close St Oswald's and relocate pupils came after a consultation in which 98% voted against the moves.
One of these was comedian and River City star Johnny Beattie, whose great niece is a pupil.
The consultation raised 11 areas of concern, with child safety being the biggest issue.
But the council said St Oswald's "effective life has expired".
SNP councillor David McDonald, who is chairman of the scrutiny committee, told the Evening Times: "The closure of St Oswald's will leave the Southside without dedicated denominational Additional Support for Learning (ASL) provision limiting parent choice.
"I have concerns that the closure is being driven by budgets rather than what is best for the education of the young people who attend St Oswald's, many of whom have suffered bullying and numerous school moves."
A spokeswoman for Glasgow City Council said: "Our experienced officers will now work with parents and teachers to ensure the smooth transition of the young people to their new school and supporting their individual needs."