Emeritus Pope Benedict XVI was on hand for the Mass, which took place just hours after Catholic bishops approved a document charting a more pastoral approach to ministering to Catholic families.
They failed to reach consensus on the two most divisive issues at the synod: on welcoming gays and divorced and civilly remarried couples.
But the issues remain up for discussion ahead of another meeting of bishops next year.
"God is not afraid of new things!" Francis exclaimed in his homily today. "That is why he is continually surprising us, opening our hearts and guiding us in unexpected ways."
He quoted Paul himself as saying the church, particularly its synod of bishops, must survey the signs of the times to make sure the church adapts methods to respond to the "growing needs of our time and the changing conditions of society."
Vatican II opened the way for Mass to be said in local languages instead of in Latin, called for greater involvement of the laity in the life of the church and revolutionised the church's relations with people of other faiths.
He is perhaps best known, though, for the divisive 1968 encyclical Humanae Vitae, which enshrined the church's opposition to artificial contraception.
That historic event marked the first time a reigning and retired pope -- Francis and Benedict -- had celebrated Mass together in public in the 2,000-year history of the church.
