But crowds in Santiago were sparser than those seen during visits to neighbouring countries, with some protesting over sexual abuse by priests and others angry at a decision made to appoint a bishop close to another who abused minors.
Francis appointed Juan Barros, a reverend who was mentored by Rev Fernando Karadima, with the latter found guilty in 2011 of abusing dozens of minors over decades by the Vatican.
Rev Barros, bishop of the southern city of Osorno, has always denied he knew what Karadima was doing when he was the priest's protege.
"It's not just time for the Pope to ask for forgiveness for the abuses but also to take action," said Juan Carlos Cruz, a victim of Karadima.
Pope Francis was greeted by President Michelle Bachelet and a band played while the two walked on a red carpet as night began to fall.
The pope travelled in a black sedan to the centre of the city, flanked by several cars. He then transferred to a popemobile, waving to small crowds of well-wishers who lined up along avenues.
Crowds were notably thin, particularly compared to papal visits in other Latin American countries.
"Long live the pope!" yelled some as he passed by in the popemobile.
Others carried signs criticising the pope or extolling him to act.
"Stop the abuse, Francis!" read one sign. "You can so you must!"
Over the next three days, Pope Francis is scheduled to celebrate Mass in Santiago, the southern city of Temuco and the northern city of Iquique.
On Thursday, the pope will go to Peru for a three-day visit.
Pope Francis' trip was aimed at highlighting the plight of immigrants and indigenous peoples and underscoring the need to preserve the Amazon rainforest.
However, sexual abuse by priests has taken the limelight in the weeks before his arrival.
Hours before Pope Francis landed, activists on issues related to sex abuse by priests called for sanctions against both abusers and anyone who helped cover up their actions.
About 200 people attended the first of several activities aimed at making the sex abuse scandal a central topic of Pope Francis' time in the country.
The majority of Chileans continue to declare themselves Roman Catholics, but the church has lost the influence and moral authority it once enjoyed thanks to the scandals, secularisation and an out-of-touch clerical caste.
"I used to be a strong believer and churchgoer," said Blanca Carvucho, a 57-year-old secretary in Santiago. "All the contradictions have pushed me away."
Local church leaders had ignored the complaints against Karadima for years, but they were forced to open an official investigation after the victims went public and Chilean prosecutors started investigating.
The Vatican in 2011 sentenced Karadima to a lifetime of "penance and prayer" for his crimes, but the church leadership has not won back Chileans' trust for having covered up his crimes for so long.
"The Karadima case created a ferocious wound," said Chile's ambassador to the Holy See, Mariano Fernandez Amunategui.
He and others inside the Vatican speak openly of a Chilean church "in crisis" as a result, a remarkable admission of the scandal's toll on a church that wielded such political clout that it helped stave off laws legalising divorce and abortion until recently.
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