He was convicted of plunder in 2007 but pardoned weeks later.
"In the end, it is the Filipino people who would act as the final arbiter on whether they would have Estrada sit again as president. It is the electorate's choice of who their president should be," the Comelec committee ruled.
Nicodemo Ferrer, the head of the Comelec committee, ruled that the constitutional ban did not apply to Estrada, saying this pertains "to an incumbent president and not to someone already previously elected".
Filipinos are due to go to the polls on May 10 for presidential, legislative and local elections.
However, signalling the legal battle may not be over, lawyer Evilio Pormento said he would appeal the ruling to the entire Comelec body.
Jose Melo, the Comelec chairman can still either uphold or reverse Wednesday's ruling.
However, Estrada said the ruling was a major victory.
"Now it's settled. Sovereignty emanates from the people and it will be the people who will decide who will be the next president," he told reporters.
"I'm very confident like in '98," he said, referring to the 1998 presidential election.
Last month three independent public opinion polls put Estrada in third place in the presidential campaign, behind front-runners Senators Benigno "Noynoy" Aquino and billionaire Manuel "Manny" Villar.