The monk, 64, set himself ablaze on Saturday during rallies against impeached President Park Geun-hye.
In his notebook found at the scene, he criticised Park's 2015 agreement to settle an impasse over Korean women forced to be sex slaves for Japanese troops during World War II in return for an apology from Japan's prime minister and a pledge of millions of dollars.
The monk was pronounced dead last night of multiple organ failures caused by his burns, according to the Seoul National University Hospital.
Park's Japan deal prompted criticism because it was announced without approval from surviving former sex slaves. Under the agreement that both countries described as "final and irreversible" at the time of its singing, Japan promised to fund a Seoul-based foundation aimed at supporting the victims.
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South Korea, in return, said it would refrain from criticising Japan over the issue and try to resolve a Japanese grievance over a bronze statue representing the wartime sex slaves that had been placed in front of its embassy in Seoul.
Seoul's Foreign Ministry said the decision was "very regrettable."
South Korea's main opposition party has stepped up calls to scrap the 2015 deal since parliament impeached Park last month over a scandal involving her confidante.
Prime Minister Hwang Kyo-ahn, who became government caretaker following Park's impeachment, said today that Seoul, Tokyo and others involved in the issue must respect the deal's spirits and try to work together to boost bilateral ties.