The petition was submitted to the office of Speaker Ramanlal Vora, senior Congress MLA Shailesh Parmar said.
It requested the Speaker to disqualify 14 rebel leaders, including Mr Vaghela, for "defying party whip and giving votes to BJP candidate in the (August 8) Rajya Sabha polls", Mr Parmar said.
"The cross-voting was a violation of anti-defection provisions in the 10th schedule of the Constitution," he said.
Though six of the rebel MLAs including Balwantsinh Rajput had resigned before the election (and therefore didn't vote), they had done so after a whip was issued by the Congress regarding the voting, Mr Parmar said.
Eight others including Mr Vaghela cross-voted and later resigned as MLAs.
Speaker Mr Vora said he hadn't seen the petition. "I am not aware of the content of the petition...I have to see the petition before making any comments," he said.
In all thirteen Congress MLAs, all loyalists of Mr Vaghela, quit the Congress ahead of or after the August 8 election, along with Mr Vaghela himself.
Ten of them have joined the ruling BJP. Mr Vaghela hasn't made his plans clear yet.
Despite cross-voting, Congress candidate Ahmed Patel defeated Balwantsinh Rajput, who was fielded by the BJP after he switched the sides.
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