The second quake happened off the island of Sulawesi at 5.02pm local time (11.02am BST), according to Indonesia's agency for meteorology, climatology and geophysics.
The agency first set the scale at 7.7-magnitude but then revised it to 7.4.
The U.S. Geological Survey put the magnitude at a moderate 6.1 and a relatively shallow 18 km.
The Indonesian government caused widespread confusion after issuing a tsunami alert on Friday afternoon, then quickly repealing at 5pm despite the tremors.
Among the country's other big earthquakes, a 6.3-magnitude quake in 2006 rocked a densely populated region of Java near the city of Yogyakarta, killing around 6,000 people and injuring 38,000.
A resident is seen beside the collapsed brick wall of her house at Tobadak village in Central Mamuju, western Sulawesi province, after a 7.5 magnitude natural disaster hit the area. The water smashed into buildings and a large mosque already damaged by the quake.
Smartphone video posted to Twitter captured a powerful wave hitting the provincial capital, Palu, as people screamed and ran in fear.
This handout photograph taken and released on September 28, 2018 by Indonesia's National Agency for Disaster Management (BNPB) shows a collapsed house following an quake in Donggala, Central Sulawesi. The tremor hit the island of Sulawesi and reportedly destroyed buildings.
A powerful natural disaster has rocked central Sulawesi in Indonesia and authorities have issued a tsunami warning.
Some people climbed 6m trees to escape the tsunami and survived, Nugroho said.
Disaster agency spokesman Sutopo Purwo Nugroho told AP that people need to be vigilant due to the aftershocks.
In this photo released by the Disaster Management Agency, a house sits damaged after a magnitude 6.1 quake early Friday, Sept. 28, 2018, in Donggala, central Sulawesi, Indonesia.
Patients are evacuated from a hospital following a strong natural disaster in Poso, central Sulawesi, Indonesia.
People can also be seen screaming and running from the rushing waters. The water smashed into buildings and a large mosque that crumpled under the force.
The city's airport remained closed after its runway and air traffic control tower was damaged but officials said they were preparing to reopen to allow aid to come in.
Some of the worst hit areas include the districts of South Banewa, Central Banewa, Sinhue and Soyol in Donggala Regency, "but we have not been able to access these areas" Sutopo said.
Indonesia sits on the Pacific Ring of Fire and is regularly hit by earthquakes.
A tsunami in 2004, triggered by an quake off the island of Sumatra, killed more than 120,000 Indonesians and 226,000 people across the Indian Ocean.
In early August a 7.0 magnitude quake struck the island of Lombok killing 82.