Officials at the Scottish Government have given the go-ahead to East Dunbartonshire Council to close St Joseph's Primary in Milngavie and build a new denominational school in a different town.
St Joseph's is the only Catholic school in the town and the Church had previously said closing it would mean a "serious deterioration" in faith school provision.
The Scottish Government had called in the decision after fierce protest from parents but has now given the go ahead.
Pupils will now be merged into St Andrew's Primary in Bearsden.
A spokesman for the Archdiocese of Glasgow said: "We strongly opposed the closure of St Joseph's Primary School and the ending of Catholic education in Milngavie.
"We share the dismay of parents, staff and pupils at this decision which will be a hammer blow for many in the affected community."
A Scottish Government spokesperson said: "Following further investigation and having looked at the totality of what has been considered by East Dunbartonshire Council in coming to its decision to close the school the Scottish ministers are satisfied that East Dunbartonshire Council has fulfilled its obligations... and that the proposal is a reasonable one which the council is entitled to make.
"Having considered carefully the information available to them on the contended inaccuracies, the Scottish ministers are content that East Dunbartonshire Council has met its statutory obligations in relation to the accuracy of information contained in its consultation documents."
East Dunbartonshire Council says it will build a new £9 million Catholic school in Bearsden.
Council leader Rhondda Geekie said: "This new school will provide a high-quality, modern learning environment for these young pupils.
"In East Dunbartonshire we have a proud record of excellence in education and we are committed to giving our young people the best educational start in life that we can give them.
"Designing the new Bearsden and Milngavie primary school to meet the needs of local people is a high priority for us and we look forward to working closely with the whole school community every step of the way on this exciting project.
"We understand the significance of primary schools for the local community. Our common goal is to ensure the best possible future education for young people in the area."