Addressing Catholic clergy, he called for a "church able to dialogue with those disciples who, having left Jerusalem behind, are wandering aimlessly, alone, with their own disappointment -- disillusioned by a Christianity now considered barren, fruitless soil."
Reaching out to those who have left the fold was a key goal of his week-long visit to the world's most populous Catholic country, where the Vatican has been alarmed by the growing strength of Evangelical Protestant churches and spreading secularism.
In a speech to prominent Brazilians, the Argentine-born pope raised the spectre of social violence in a country rocked last month by massive street protests demanding an end to corruption and a better life.
"Constructive dialogue... (is) essential for facing the present moment," Francis told political, religious and civil society leaders assembled in Rio's Municipal Theatre.
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"Between selfish indifference and violent protest there is always another possible option: that of dialogue," he said.
Since his installation in March, the first Latin American pope has sought to re-energise Catholics, using his Rio trip to urge young believers to spread the Gospel and "make a mess" in their dioceses.
During a nine-kilometre (5.5-mile) march to the Cabana beach venue for Saturday night's vigil, many agreed that the church needed a dose of energy, lamenting that too many have lost interest in an institution hurt by paedophilia and financial scandals.
Some suggested social media could help spread the Gospel while others said young Catholics needed to be more active, join missions and open up about their faith.
"Oh yeah! Shake it up, big time! You have to," said Adrian Antonio Flores, a 31-year-old from the US state of Minnesota who works for a website catering to young Catholics.
Earlier, the pope used a mass to challenge priests to bring the message of the Gospel to the world's slums as he pressed his drive to revive a struggling Catholic faith.