Simeon based his ruling on Leingkone having missed three consecutive sittings of Parliament while he received medical treatment in South Korea.
The Speaker's ruling at that time allowed him to avoid a vote of no confidence, with only 25 MPs on both sides of the House.
The Supreme Court on Thursday declined Leingkone's petition for a stay on the Speaker's decision to declare his seat vacant.
Leingkone's lawyer had argued that only the Supreme Court could declare a parliamentary seat vacant, and he maintained that the MP was only absent for two regular sessions, with the third being an extra-ordinary session, called at short notice.
The opposition has since filed a motion of no confidence in the newly installed prime minister Sato Kilman and that is set to be debated by parliament on next Monday.
Kilman, who has been prime minister four times previously, came to power just three weeks ago after the then sitting prime minister Ishmael Kalsakau was removed in a vote of no confidence.
RNZ Pacific correspondent in Vanuatu Hilaire Bule reports that both sides, which are in camps near the capital, continue to have 25 MPs each.