However Tropical Storm Mekkhala, which was expected to bring much more intense rain to the region in the afternoon, forced the pope to cut short his trip.
In the town of Palo, about 12 kilometres (seven miles) from Tacloban, he told a crowd of thousands who had gathered at the main church that he needed to leave quickly to avoid the storm.
“So I apologise to you all. I’m sad about this, truly saddened. Because I had something prepared especially for you,” he said.
His motorcade then raced back to the airport and he departed shortly after 1:00 pm (0500 GMT), four hours earlier than scheduled. However the main event of the day was the morning mass.
The Philippines endures an average of about 20 major storms a year, many of them deadly.
But the unprecedented strength of Haiyan, with winds of 315 kilometres an hour, was an extreme weather event consistent with man made climate change, the United Nations’ weather agency and scientists have said.
The Philippines has long been the Church’s stronghold in the region, with Catholics accounting for 80 percent of the former Spanish colony’s population.
Massive crowds gathered along the pontiff’s motorcade routes during his first two days in the Philippines.
Pope mania was expected to reach a peak on Sunday, with organisers expecting him to attract as many as six million people for mass at a Manila park.
If as big as expected, the crowd will surpass the previous record for a papal gathering of five million during a mass by John Paul II at the same venue in 1995.