He however said that although he is resigning from the post he would continue to work as a back-bencher in Parliament.
Making a special statement in Parliament, before announcing his resignation, Karunanayake said all the allegations leveled against him were "baseless" and he had resigned to protect the image of his government.
But Opposition lawmakers and sections of civil society had demanded the Foreign Minister resign immediately, accusing him of corruption and hindering transparency.
Some political analysts say that former Foreign Minister Mangala Samaraweera is also being considered.
"I am proud of creating such a situation in the country", the Premier said.
President Maithripala Sirisena's government has pledged to end the rampant corruption that affected the Indian Ocean island's previous government.
The allegations followed Karunanayake's appearance before the panel last week, and he has not been charged by any court.
Ravi Karunanayake, 54, stepped down from the cabinet amid questioning over his connection to an insider trading scandal at Sri Lanka's central bank after the new government was elected in January 2015. A month after they formed the government, a massive scam at the Central Bank came to light.
Mahendran was accused of misconduct surrounding alleged favours for his son-in-law, Arjun Aloysius, a bond dealer.