Haneen Zoabi is expected to appeal to Israel's highest court which has overruled most previous efforts to disqualify Palestinian candidates as violations of free speech.
Israel's Central Elections Committee voted 19 to 9 with one abstention to block Zoabi's candidacy for the Jan. 22 general election, a committee spokesman said. Separate motions to disqualify two Palestinian political parties were defeated.
Zoabi was on board the Mavi Marmara ship which was boarded by Israeli troops as it approached waters off Gaza in May 2010 as part of an international flotilla challenging Israel's blockade on the enclave.
Nine Turkish citizens were killed, striking a huge blow to relations between the two countries.
The electoral committee disqualified Zoabi on two grounds: "negating Israel's existence as a Jewish state" and "support for an enemy state or terrorist organization engaged in armed conflict against Israel," spokesman Giora Pordes said.
Centrist and left-leaning Israeli lawmakers argued against disqualifying Zoabi.
"We cannot deny representation to people who disagree with us," said Nitzan Horowitz of the left-wing Meretz party.
Zoabi belongs to a tiny party in Israel's parliament that believes the country should not be defined as a Jewish state, which it sees as discriminatory toward the minority Palestinian population.
Most of the Palestinians who make up about 20 percent of the Israeli population are related to or descended from Palestinians who fled or were driven away in a 1948 war over Israel's establishment.
Zoabi has insisted she had no role in any of the violence on board the Mavi Marmara and had tried to mediate between the sides.
JERUSALEM (Reuters) -- Israel's electoral authority barred a Palestinian lawmaker from re-election on Wednesday, saying she had supported the nation's enemies by joining a protest ship that tried to break a naval blockade of Gaza.