Protestants, Catholics and Charismatics make up about 10 percent of the population of Palu, where neighborhoods and miles of coastline were obliterated by the Sept. 28 quake and tsunami.
At least 200 people including soldiers filled the grey pews of the Protestant Manunggal church in Palu for the second of three services planned Sunday.
They sang as a young girl in a black and white dress with a red bow danced in the aisle, prayed and listened to a 30-minute sermon from the priest, Lucky Malonda. A woman in the frontmost pew wept.
Indonesia's disaster agency said on Saturday that the death toll had climbed to 1,649 with at least 265 people still missing, though it said that number could be higher. Bodies are still being recovered from neighborhoods where the force of the quake liquified the earth and sucked houses into the ground.
Min Kapala, a 49-year-old teacher, said she came to the city of more than 25 churches from an outlying area because her usual house of worship was destroyed.
Outside the church, Malonda said the intensity of the disaster had taken even scientists by surprise and called it the will of God. Two people from his congregation were missing, he said.
Malonda said religious leaders are discussing holding inter-faith prayers but nothing has been agreed yet.
Central Sulawesi, of which Palu is the capital, has a history of violent conflict between Muslims and Christians, though tensions have calmed in the past decade.
In the Indonesian capital, Jakarta, people walked around thoroughfares empty of cars collecting donations for earthquake victims during the weekly car free morning in the city center.
Roadside restaurants were open in Palu but long lines of cars and motorcycles still snarled out of gas stations.