Mr Mani was accompanied by former Kerala Chief Minister Oommen Chandy, Opposition leader in the Kerala assembly Ramesh Chennithala and Indian Union Muslim League leader MK Muneer, when he filed his papers before Legislature Secretary VK Babu Prakash.
Mr Mani is currently the only member of Kerala Congress (M) in the Lok Sabha. Kerala Congress (M) snapped ties with the United Democratic Front two years ago, amid rift over a corruption scam.
The June 7 decision of the Congress to hand over the sole Rajya Sabha seat to Kerala Congress (M) had triggered strong protests from a section of party leaders in the state, including young legislators and a former state Congress chief.
"This is truly disappointing, not only for me and fellow MLAs but also party workers on the ground. They feel this is an insult to their spirit," Congress lawmaker VT Balram told NDTV. "The seat has gone to another political party which is not even a part of the Congress in Kerala right now. Kerala Congress (M) aligned with the CPM in the Kottayam local body and also attended the CPM plenary session," he said.
Congress leader and Rajya Sabha Deputy Chairman PJ Kurien and former Kerala Pradesh Congress Committee Chief VM Sudheeran were in the forefront in attacking the decision, which they said lacked transparency and had been taken without taking the party into confidence.
"This is an abject surrender by the Congress," Mr Kurien reportedly said, accusing senior party leaders of misleading Congress President Rahul Gandhi. Mr Kurien is said to have written to Rahul Gandhi suggesting that if not him, the party should nominate another Congress leader for the seat. He is also said to have suggested the names of six leaders.
Meanwhile, CPI(M) leader Elamaran Kareem and CPI leader Binoy Viswam filed their nomination papers for the Rajya Sabha polls as the candidates for the ruling CPI(M)-led Left Democratic Front.
Chief Minister Pinarayi Vijayan, LDF Convener A Vijayaraghan and CPI State Secretary Kannam Rajendran were among those present when they filed the papers.
With the retirement of Rajya Sabha Deputy Chairman PJ Kurien, CP Narayanan of CPI(M) and Joy Abraham of Kerala Congress, three Rajya Sabha seats from Kerala will fall vacant on July 1. Of these, the ruling Left Democratic Front is poised to win two and the United Democratic Front, one.
(With inputs from PTI)