The EC had petitioned the joint law-review committee set up last month to reconsider the bill, but the panel resolved to retain all six points as set out in the original, insisting that none violated the Constitution.
EC president Supachai Somcharoen, also a member of the joint panel, was alone in calling the bill unconstitutional.
After a two-hour debate between Supachai and the other joint committee members, the NLA passed the bill by a 194-0 vote, with seven abstentions.
The bill, which now goes to the Cabinet, would result in EC members being removed from office once a new slate of commissioners was seated.
The EC has the right to petition the Constitutional Court to review clauses it regards as unconstitutional.