St Oswald's Secondary School will now be sited at a new campus shared with St Margaret Mary's Secondary in Castlemilk.
Parents, staff, church leaders and the local community have all been involved in discussions about the move since the launch of consultations last May.
More than 450 letters of objection to the move were handed in to the council.
The relocation of the 118-pupil school, for young people with additional support needs, will provide inclusion opportunities for the pupils in both schools, said the council.
Councillor Stephen Curran, the executive member for education and young people, said: "As well as the formal responses to the consultation, we've been listening to the parents' ideas, opinions, concerns and suggestions as to how we can best meet the needs of all of St Oswald's young people.
"The school, to be relocated to a separate wing and within existing capacity in St Margaret Mary's Secondary, will retain its own identity but there will now be the opportunity to extend the curriculum for the young people - something that wasn't possible in their current building.
"St Oswald's pupils will now be able to access an extended range of secondary subjects and utilise the state-of-the-art facilities in the St Margaret Mary's building."
Officers will continue discussions with parents and families about transition arrangements for each pupil to ensure the best educational outcomes as part of the move.
The St Oswald's pupils will stay in their own building until June 2014 but will be able to visit their new building to get to know it before they start there in August 2014.