The pontiff visited Sri Lanka and the Philippines on his second trip to Asia in five months, seeking to promote the Catholic Church in one of its most important growth regions.
Tens of thousands of people in the Philippine capital of Manila crowded his motorcade route on Monday morning for a final glimpse of Francis, and he smiled and waved to them from an open-air "popemobile".
President Benigno Aquino then led a red-carpet farewell on the tarmac at the airport, as children sang and danced, before the pope gave a final wave to the Philippines and boarded his plane to return home.
Sunday saw one of the highlights of his Asian journey, with six million people turning out in Manila as he celebrated mass -- a world record for a papal gathering.
The Philippines is famed as the Catholic Church's bastion in Asia, with 80 per cent of the former Spanish colony's 100 million people following the faith.
But even the pope was stunned at the size of the crowd, which surpassed the previous world record of five million during a mass by John Paul II at the same venue in 1995.
"I cannot fathom the faith of the simple people," Francis said, according to the archbishop of Manila, Cardinal Luis Antonio Tagle, who acted as the pontiff's chaperone during his five days in the Philippines.
Throughout his time in the Philippines -- where a quarter of the population lives on 60 cents a day or less -- the pope spoke out against the forces that entrench poverty.