QGIS » QGIS Application

Load the following GeoJSON

{
  "type": "FeatureCollection",
  "features": [
    {
      "type": "Feature", "properties": {},
      "geometry": { "type": "Polygon", "coordinates": [[
        [ 0, 0, 0 ],
        [ 1, 0, 0 ],
        [ 1, 1, 0 ],
        [ 0, 1, 0 ],
        [ 0, 0, 0 ]
        ]]
      }
    }
  ]
}

and inspect the metadata:

Geometry type of the features in this layer
Polygon (WKB type: "PolygonZ")

You see it has a z-dimension.

Now save the layer as new GeoJSON file, force the geometry type to Polygon and untick "Include z-dimension".

The new file will still include the z coordinates even though we told QGIS to not include it.

This does not happen when saving to Shapefile, I did not try others. The GeoJSON spec allows a third element in the coordinates array so the input seems to be valid.