The wind caught the pope's white skullcap and ripped the cassock underneath his plastic poncho as he spoke to those gathered at the main cathedral in Leyte Province.
"I felt that I had to be here ... I am here to be with you, perhaps a little late, I have to say, but I am here," he said, according to Reuters:
"Many of you have asked the Lord, 'Why?' And to each of you the Lord is responding to your hearts from his heart ... so many of you have lost everything. I don't know what to say to you but the Lord does know what to say to you."
"Nearly 3,000 victims are buried in the city's almost half-hectare mass grave site. Hundreds are still unaccounted for.
"I am sad about this, truly saddened, because I had something prepared especially for you," he said, adding that instead, he barely had time to get back to the airport.
A 27-year-old woman who was volunteering with Catholic Relief Services and attended the gathering of 150,000, was killed when a sudden gust of wind toppled a scaffolding following the Mass, The Associated Press says.
As many as 6 million people are expected for the pope's Sunday Mass in Manila. The pope is on the first leg of a six-day visit to Asia. He is scheduled to visit Sri Lanka next.