The ruling Congress, on the other hand, claimed a moral high ground, saying the United Progressive Alliance minister tendered his resignation in highest traditions of democracy and hoped that the opposition would now let Parliament to function.
Tamil Nadu Chief Minister and Dravida Munnetra Kazhagam supremo M Karunanidhi said he had directed Raja, "my affectionate brother", to quit "only to allow the functioning of Parliament".
Describing it as the "mother of all scams" and "a monumental fraud of 1.76 lakh crore", Bharatiya Janata Party chief spokesperson Ravi Shankar Prasad said Raja must be prosecuted under the Prevention of Corruption Act.
"A proper FIR should be lodged, The Central Bureau of Investigation is already inquiring. All those involved in this big scam...should be made accountable and liable. All should be prosecuted," he said.
BJP spokesperson Rajiv Pratap Rudy said, "The acceptance of Raja's resignation by the PM vindicates BJP's position ...but this does not absolve the government of the charges of corruption engulfing it in the recent past.
"The BJP still reiterates its demand for a Joint Parliamentary Committee probe and the Prime Minister -- Mr Clean -- has to do a lot of answering to the charges of corruption against the Congress government," he said.
The All India Anna Dravida Munnetra Kazhagam, the main opposition party in Tamil Nadu whose supremo Jayalalithaa had offered its support to UPA in return of "sacking" of Raja, termed it a "a victory for democracy".
"Madam's (Jayalalithaa) interview last week (offering support), had a catalytic effect on the whole episode.
Raja's resignation today is a victory for democracy. It is a victory for probity in public life and a victory for crusade against corruption," AIADMK leader V Maitreyan said.
"It is only the beginning, not the end of it. Raja's resignation is only the first step. Now that he has resigned, cases should be filed against him under Prevention of Corruption Act, he should be prosecuted and law should take its own course," he said.
The Communist Party of India-Marxist said the resignation is not the "end in itself". "We have been asking for this for over two years. This is not the end in itself as resignation was sought for conducting an impartial inquiry into how the system was manipulated to cause such a massive loss. Impartial inquiry is required to cleanse the system," CPM leader Sitaram Yechury said.
CPM general secretary Prakash Karat said with the resignation of Raja it is imperative that the probe into the scam is conducted thoroughly so that "those guilty of causing such a huge loss to the exchequer are brought to book".
The opposition parties gave enough indications that they will continue to raise the issue vociferously in Parliament, saying the matter did not end and the Prime Minister will have to do a lot of answering.
Congress, meanwhile, expressed confidence that Raja's resignation will have no bearing on its alliance with DMK. Party spokesperson Jayanti Natarajan said that the resignation showed that UPA was maintaining highest standards of accountability and integrity.
She recalled that for the last one week, the opposition had obstructed Parliament on the issue and hoped that they would now allow Parliament to function properly.
Replying to questions, Natarajan said that her party's alliance with DMK is "very strong" and there will be "absolutely no change" in it. "There can be no bearing on Raja's resignation on the alliance," she said.