Councillors in East Renfrewshire voted unanimously to drop the proposals for Newton Mearns, south of Glasgow, after it generated a significant public response.
Plans for a joint campus in Newton Mearns, including Jewish and Catholic primary schools, the first in Scotland, were approved at the same meeting.
The opposition Tories in East Renfrewshire asked questions about the traffic impact on the new school but did not oppose the cancellation of the mosque plans.
The Herald revealed on Saturday details of the report which led to the cancellation of the plans.
It read: "In view of the volume of representations received, the sensitivity concerning the proposal and the extremely wide range of issues raised, it is recommended that this proposed modification be pursued no further and is not included in the plan."
The proposals for the mosque had been put forward by the local Muslim community as they had no permanent place of worship in Newton Mearns, despite demand for more than a decade. The community had suggested land next to the new Eastwood High School was its preferred site.
The Scottish Government's Reporter, who adjudicates on planning issues, had been critical of the length of time it has taken local Muslims to secure a permanent place of worship and allowed temporary change of use of a former nearby British Legion club for Muslim prayer services.
Parents had concerns at the possibility of protests outside the school and the potential for vandalism, fireraising or bomb attacks from far-right extremists.
Council leader Jim Fletcher said: "We will now revert to our original local plan and identify a site for development which will include a permanent place of worship for our growing Muslim community."