Rajput, who quit the Congress ahead of the August 8 election, also contended that votes of two other Congress MLAs should be discounted, and he should be declared winner.
The EC's decision paved the way for the victory of Congress candidate Ahmed Patel -- who got 44 votes, the minimum he needed to win -- in the high-stakes electoral battle. Rajput polled 38 votes.
Rajput's petition claimed that once the Returning Officer had used his discretion to accept the two votes as valid, the EC had "no power to issue any direction to the Returning Officer for accepting or rejecting any vote".
The EC had rejected the votes of former Congress MLAs Raghavji Patel and Bholabhai Gohel.
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Congress's polling agent Shaktisinh Gohil had lodged a complaint before the counting began that these two MLAs showed their ballots to BJP representatives before putting them in the ballot box.
MLAs are not allowed to show their ballots to anybody other than the authorised polling agent of their own party, the Congress leader said.
Rajput's petition said that EC's order should be set aside, as it was "patently illegal".
Once the Returning Officer had exercised his discretion of accepting these two votes as valid, the EC had no power to hear any appeal against the order. The only remedy the aggrieved party had was to move a court, it said.
Two other MLAs of Congress had also shown their ballots to unauthorised persons, and these two votes, which went to Patel, must be held invalid, the petition said.
If these two votes were rejected, Rajput would get more votes, and hence he should be declared as elected to Rajya Sabha in place of Patel, the petition said.