But the NLD now faces dissolution in less than six weeks for failing to register, according to legislation recently brought in for elections due to be held by the end of November.
"The National League for Democracy has decided not to register the party," party spokesman Nyan Win said after a meeting of more than 100 senior members at NLD headquarters in the economic hub Yangon.
Under election legislation dismissed as a sham by international critics, if the party had decided to sign up for the vote it would have been forced to part with Suu Kyi because she is serving a prison term.
The Nobel peace laureate, who has been locked up for 14 of the last 20 years, had already told the party she was opposed to such a move.
"Our aim is not the NLD party's existence in law. We are focused on the survival of our politics. Today our members made their decision in accordance with Suu Kyi's message," Nyan Win told reporters.
Before the vote, Nyan Win read a message from Suu Kyi to senior members in which she reiterated her opposition to the "unjust" law.
"If the NLD is dissolved, one cannot assume the NLD will deteriorate," she said, according to the message, adding that the NLD "is not my own thing, nor anyone's possession".
The election is part of the government's seven-step "Roadmap to Democracy," which also includes a controversial new constitution agreed in a 2008 referendum held days after a cyclone ravaged the country.
Myanmar's election law nullifies the result of the last polls held in 1990 that were won by the NLD by a landslide but never recognised by the junta, which has ruled the country since 1962.
Myanmar political analyst and pro-democracy activist Win Min said the party -- which Suu Kyi helped found in 1988 after a popular uprising against the military government -- would now essentially disappear.
"The party, under its current name, might not officially exist after the May 6 deadline," Win Min said.
"It was very hard for the NLD members to exclude her (Suu Kyi) because she is a very influential figure in the party and in the country," he said.
Tin Oo, the party's number two, denied the decision was the end for the party. "There are many peaceful ways to continue our activities," he said.
In all, 115 party representatives attended the meeting as dozens of rank-and-file members gathered outside amid tight security, some wearing white tops bearing the slogan: "We believe Aung San Suu Kyi".
"We have sacrificed our life for 20 years and finally we have to give up like this. So you can imagine how we feel in our hearts," said Nann Khin Htwe Mying, a senior NLD member who arrived for the talks from eastern Karen state.
The United States, which has led international criticism of the new election law, blamed the junta for the opposition's decision to boycott, saying the regime had missed an opportunity.
"This is a reflection of the unwillingness of the government in Burma to take the necessary steps to open up the political process," State Department spokesman Philip Crowley said, referring to Myanmar by its former name.
But he indicated that Washington would continue dialogue begun under President Barack Obama's administration, despite its failure to persuade the junta to change course on the election.
"I don't know that we expected necessarily everything to be resolved in one or two or three meetings," Crowley said.
Junta chief Senior General Than Shwe warned Saturday against "divisive" and "slanderous" election campaigning as he presided over an annual military parade.
Suu Kyi is one of more than 2,000 political prisoners in Myanmar, which remains under US and European sanctions over its human rights record.
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