This should work if your spatial table is "geo_table" and using SRID=4326, geometry column is "geometry", and coordinates are in table "coord_table" in columns "X" and "Y"
update geo_table a set a.geometry=
(select
(MDSYS.SDO_GEOMETRY(2001,
4326,MDSYS.sdo_point_type(b.X,b.Y, NULL),NULL, NULL))
from coord_table b
where a.id=b.id);