Early reports indicate at least nine people have been killed and more than 40 injured, while hundreds of buildings have been badly damaged across several cities, and phone lines and electricity have gone down in many regions.
Tsunami warnings were repeatedly issued and lifted in the hours following the earthquake, as many people ran inland fearing a repeat of the 2004 tsunami.
Thursday's magnitude-7.8 quake hit the same area in southern Sumatra as Wednesday's quake.
The second quake struck at 06.49 on Thursday (23.49 GMT on Wednesday), about 10km (six miles) under the sea, the US Geological Survey has said.
Casualties appear to be lower than first feared, but officials warned that bad communications may be hiding the scale of the impact.
Wednesday's quake led to tsunami warnings being issued across the Indian Ocean, but only a small wave surge of about 1m (3ft) hit Sumatra, causing little damage.
At least a dozen aftershocks were felt later and four more tsunami warnings were briefly declared and then lifted, reports from the region have said.
The first quake could be felt 375 miles away in Indonesia’s capital Jakarta where office workers reportedly rushed down the stairways of tall, swaying buildings. High rises in neighboring Malaysia, Singapore and Thailand also swayed due to the earthquake.
