The nomination of K Padmarajan was rejected as some documents required to be filed were not submitted.
With this, decks have been cleared for the election of CPI-M's Elamaram Kareem, CPI's Binoy Viswam, both candidates of the Left Democratic Front, and Jose K Mani of the Kerala Congress.
The official announcement of their election would be made tomorrow, the last date for the withdrawal of nominations, sources said.
"If nobody withdraws nominations, all three will be declared elected tomorrow," they said.
Polling for the biennial election for three Rajya Sabha seats from the state is scheduled for June 21, but it looks unlikely now.
Mr Mani is currently the lone Kerala Congress (M) member in the Lok Sabha.
The Congress' decision to forego its claim to the one RS seats it could have won easily, and hand it over to KC(M) to pave the way for its return to the Congress-led UDF, had raised the hackles of many in the main opposition party.
Jose K Mani is the son of KC(M) supremo K M Mani, who had snapped ties with the Congress two years ago, accusing the alliance spearhead of insulting his party.
The state Congress leadership had come under severe criticism from Kurien, former KPCC chief V M Sudheeran and some sitting MLAs for the decision of not fielding its candidate and back the KC(M) nominee.