He has written to Education Secretary Michael Russell asking for the decision to be called in for scrutiny.
The move comes after councillors from East Dunbartonshire backed plans to close St Joseph's Primary in Milngavie, on the outskirts of Glasgow.
Under the proposal, pupils will go to a new school in neighbouring Bearsden following a merger with
St Andrew's Primary.
The council acted against a backdrop of falling school rolls and funding cuts, and wants to make £20 million savings over the next three years.
However, parents and the Church say rolls have increased in recent years and argue the move will leave Milngavie with no Catholic primary school.
Archbishop Tartaglia is asking Mr Russell to act under education legislation.
In his letter to Mr Russell, Archbishop Tartaglia said: "I greatly regret to say that, despite our best efforts, the council has proceeded with a decision which I believe to be manifestly unjust and discriminatory against Catholic children and parents in this community.
"While the council appears content to provide three non-denominational schools in the town of Milngavie and one in Baldernock, there will be no Catholic school provision if this decision stands."
Gordon Currie, director of education for East Dunbar-tonshire, said St Joseph's roll had dropped by 23%in the last decade.
He said: "This proposal, to provide one modern, well-equipped school to replace two very under-occupied schools ... represents a significant investment in Catholic education of almost £9m."