The reopening had been set for December 1 but was postponed as the highly contagious Covid-19's Omicron variant spread.
Less than a thousand new cases were added daily during the Christmas holidays, when large crowds of shoppers trooped back to malls and restaurants, despite constant government warnings.
The subsequent surge peaked above 39,000 infections in one day in mid-January but has since eased.
Health officials reported about 3,600 infections on Wednesday, with 69 deaths, and have declared the entire archipelago, except for one southern region, at "low to moderate risk".
More than 60 million of nearly 110 million Filipinos have been fully vaccinated against Covid-19 and 8.2 million have received their booster shots in a campaign that has been hampered by vaccine shortages and public hesitancy.
President Rodrigo Duterte warned Filipinos in televised remarks on Monday that "we are not over the hump" and urged the unvaccinated to get immunized soon.
"You can walk around and, if you get contaminated, you will be awfully very, very sorry for yourself and your family."
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