Worshippers in ponchos of all colors held up flickering candles in the rain, hanging on his every word.
The Pope wore a yellow poncho over his robe as he celebrated the Mass, which was attended by 6 million people, according to the Philippine News Agency.
"May he enable all the beloved people of this country to work together, protecting one another, beginning with your families and communities," the Pope said.
His homily followed a thunderous welcome to the capital.
As he entered the park, the huge crowd chanted, "Papa Francesco, Papa Francesco!"
He waved, kissed babies and reached over to touch the hands reaching out to him.
'We are all God's children'
The Pope's message included one he's talked about many times: empathy.
"In these days, throughout my visit, I have listened to you sing the song 'We are all God's children,'" he said. "All of us are God's children, members of God's family."
Young people, he said, especially need extra care.
"Jesus himself needed to be protected," he said.
"We too need to protect, guide and encourage our young people, helping them to build a society worthy of their great spiritual and cultural heritage," he said.
As Francis left the venue in the capital, some jumped over barricades and ran after his vehicle.
"We love you, Papa Francesco!" others yelled.
Heavy rains pounded the city ahead of the Mass. Tropical storm-force winds howled just east of the event venue.
The nation intensified security at all venues, with the presidential detail deployed to safeguard the Pope.
About 25,000 Philippine national police are backing the presidential security detail tasked with safety for the event, authorities said.
"We are putting our best foot forward in this historic national event," said Leonardo Espina, the deputy director general of the national police.
"We have rehearsed and fine-tuned all our systems and procedures for this event, such that we have established full backup system that will address any unforeseen situation that may arise."
Firearms were prohibited in all areas holding events linked to the papal visit, including the routes his entourage would use.
Trip cut short
A day earlier, the Pope cut short his trip to Tacloban as an approaching typhoon with blistering winds threatened the Philippine city about 600 kilometers (370 miles) southeast of Manila.
Tacloban is still recovering from the 2013 disaster of Super Typhoon Haiyan, described as one of the strongest storms ever recorded with 195-mph sustained winds. It killed 6,300 people nationwide.
Typhoon Mekkhala, which is called Typhoon Amang in the Philippines, made landfall Saturday afternoon just northeast of Tacloban.
Francis donned a slicker to celebrate Mass in Tacloban on Saturday for hundreds of thousands who gathered despite the stormy weather.
Mekkhala was downgraded Sunday, but was still packing winds up to 45 mph and heavy rains.
A call for social justice
The Pope's trip began Tuesday in Sri Lanka; he landed in the Philippines on Thursday.
On Friday, he met with President Benigno Aquino, and the pontiff urged the political leader to reject corruption and promote "honesty, integrity and commitment to the common good," the Vatican said.
He also called for social justice and respect for human dignity, according to a copy of his remarks provided by the Vatican.
"Here in the Philippines, countless families are still suffering from the effects of natural disasters. The economic situation has caused families to be separated by migration and the search for employment, and financial problems strain many households," he said.
"While all too many people live in dire poverty, others are caught up in materialism and lifestyles which are destructive of family life," the pope said.
He plans to leave Manila for Rome on Monday.