Oh wow, i feel so stupid by ready all this answers, they are like experts' answer with all CTE and temp table and etc.
And all I did to get it working was simply aggregated the ID column by using MAX.
DELETE FROM table WHERE col1 IN (
SELECT MAX(id) FROM table GROUP BY id HAVING ( COUNT(col1) > 1 )
)
NOTE: you might need to run it multiple time to remove duplicate as this will only delete one set of duplicate rows at a time.