"It is in the favelas ...That we must go to seek and serve Christ," he told thousands of bishops, priests and seminarians from around the world gathered for a mass at Rio's St Sebastian Cathedral.
"We cannot keep ourselves shut up in parishes, in our communities, when so many people are waiting for the Gospel," Francis said.
"In many places, the culture of exclusion, of rejection is spreading. There is no place for the elderly or for the unwanted child. There is no time for the poor person on the edge of the street," he added.
Addressing the Catholic clergy, he said "have the courage to go against the tide."
"Encountering and welcoming everyone, solidarity and fraternity: these are what make our society truly human," he said, denouncing human relations based on "efficiency and pragmatism".
Later in the day, Francis was to join hundreds of thousands of young pilgrims attending World Youth Day (WYD) in a prayer vigil on Rio's Copacabana beach.
Security was tight across central Rio with gun-toting army troops backing up police units.
Meanwhile, thousands of Catholics attending the Catholic youth festival ignored the cold, rainy weather and set off on a nine-kilometre (5.4 miles) walk across the city to reach the beach venue for the evening vigil.
There they will pray and spend the night before attending tomorrow's mass with the pope at the close of the Catholic youth fest.
Yesterday, the 76-year-old pontiff and some 1.5 million faithful that gathered to see him watched a somber re-enactment of the stations of the cross depicting scenes of a bloodied Jesus as he was led to his crucifixion.
Last month, young Brazilians spearheaded massive street demonstrations against political corruption, to demand better public services, and to protest the high cost of hosting next year's World Cup.
