Party chief Vaiko had on Thursday expelled the rebel MPs from the MDMK.
Party leader C Krishnan filed the petition before the Lok Sabha secretary general P D T Achary seeking disqualification of L Ganesan and Gingee Ramachandran for going against the party whip and supporting the United Progressive Alliance government in the crucial trust vote.
"When the party issued the direction to its MPs to vote against the confidence motion, Ganesan and Ramachandran voted contrary to the party's direction which attracted provisions of the Tenth Schedule of the Constitution, making them liable for disqualification," Krishnan said.
The two dissident MPs had revolted against the party leadership for aligning with All India Anna Dravida Munnetra Kazhagham in the 2006 assembly polls and functioned independently after they were removed from the party posts.
The rebel MPs had also approached the Election Commission to declare their group as the real party. But the EC had recently ruled that the party led by Vaiko was the genuine MDMK.