The typhoon killed at least 76 people and left millions without electricity and drinking water, as well as causing major damage to agricultural land and key infrastructure.
The composite index fell 14.02 points to 2,542.69, off a low of 2,517.84 and a high of 2,554.07.
The broader all-share index fell 4.47 points to 1,548.12.
However, gainers beat losers 45 to 34, with 47 stocks unchanged.
Turnover was 2.6 billion shares worth P7.39 billion.
"A lot of businesses likely suffered losses in the widespread power outage in the last four days. Communication lines were also damaged," said Ron Rodrigo of Unicapital Securities.
"Investors took this situation as an excuse to take profits," he said.
Manila Electric Co. (Meralco), which supplies electricity to Manila and nearby provinces, said power has been restored to about 94 percent of its franchise area.
Fallen trees and other debris has however slowed down restoration work, it said.
Meralcos A shares ended 50 centavos higher at P19.75, recovering from losses early in the session. Its B shares were steady at P29.50.
Philippine Long Distance Telephone Co. (PLDT), the most actively traded stock, fell P20 to P2,250.
Conglomerate Ayala Corp. was down P10 at P465.
Food and beverage giant San Miguel Corp.s A shares were unchanged at P65 while its B shares were 50 centavos higher at P76.50.
Jollibee, the nations biggest fast-food company, fell P1, or 2.8 percent to P34.50.
"The power outage forced shopping malls to close," said Jerome Gonzales, who helps manage $20 million at PhilEquity Fund in Manila. "Thats going to hurt sales at retailers and restaurants.
Equitable PCI Bank declined P6, or eight percent to P69.50, after Philippine tycoon Henry Sy said shareholders agreed to sell him 52 percent of the company, raising his stake to 86 percent. Sy has said he may merge Equitable into his Banco de Oro. AFP