You are looking for a GP tool Create SQLite Database available since 10.4 (previously, in 10.3, you had to use an arcpy function CreateSQLiteDatabase().
Choose as spatial_type parameter GEOPACKAGE which will create an OGC GeoPackage dataset. This is essentially an SQLite database with ST_Geometry storage plus some extra OGC features.
You can use this workspace very much like any SQLite geodatabase, that is load/export feature classes and tables and create views. You can read more about support for SQLite in ArcGIS in this help topic SQLite and ArcGIS.