All 190 lawmakers present voted in favor of the repeal. There are a total of 300 lawmakers in the parliament.
Won-shik's office said the president's declaration of martial law was invalid following the lawmakers' vote.
The speaker has also urged the president to immediately lift martial law.
Earlier, the country's President Yoon Suk Yeol declared emergency martial law in a live televised address to the nation.
The president held an emergency meeting in his office overnight, after which he announced the imminent paralysis of power due to attempts to impeach him, according to the Yonhap news agency.
"The activities of the National Assembly and local legislative assemblies, as well as political parties, political gatherings, rallies, demonstrations and other political activities are completely prohibited," the Decree No. 1 of the Martial Law Command, which was signed by General of the Army of the Republic of Korea Army Park An-su, read.
The commander of the martial law in South Korea also said that control over all media outlets is being introduced in the country.
The South Korean Defense Ministry has ordered commanders of all military branches to increase combat readiness.
Footage has emerged online showing South Korean Armed Forces entering the country's Parliament.
The troops of the martial law command are trying to enter the parliament building, and the main entrance to the National Assembly is blocked, and barricades are being installed, according to Yonhap.
The situation near the parliament is extremely chaotic now, the passage to the territory adjacent to the National Assembly is blocked, admission is carried out only after checking identity cards, a number of deputies were unable to enter the territory of the complex. At one of the entrances there is a large bus with the inscription "Land Forces of the Republic of Korea". More than 100 people are gathered in front of the parliament building.
The South Korean military said it has been fighting "anti-state" forces. The defense ministry has ordered the army to be ready to repel emergency situations, reserve soldiers to go on duty, media reports say.
Videos from social media show clashes taking place near the parliament's building.
The military has left South Korea's parliament building, the Yonhap news agency reported, citing the speaker of the South Korean parliament, Woo Won-shik.