After the 7.6-magnitude aftershock struck just before midnight Wednesday, Chile's Emergency Office and navy issued a tsunami alert and ordered a precautionary evacuation of low-lying areas for the country's whole 2,500-mile (4,000-kilometer) Pacific coastline.
Among those moved inland was President Michelle Bachelet, who was in the city of Arica assessing damage in the north from Tuesday night's powerful quake.
"I was evacuated like all citizens. One can see that the people are prepared," she tweeted early Thursday.
Chile's evacuation order was lifted at around 2 a.m. Thursday. The whole coast also was evacuated for several hours after Tuesday's quake, and for the night in the north, although the tsunami proved small.
The aftershock caused buildings to shake and people to run out into the streets in the port of Iquique, which was one of the cities that suffered damage from the Tuesday earthquake. There were no immediate reports of serious damage or injuries from the aftershock, which was one of dozens that have followed the magnitude-8.2 quake.
State television said the aftershock caused some landslides near Alto Hospicio, a poor area in the hills above Iquique where about 2,500 homes were damaged by Tuesday' earthquake.
The Ministry of Education suspended classes again in schools in the north for Thursday.
The aftershock was felt across the border in southern Peru, where people in the cities of Tacna and Arequipa fled buildings in fear. Police Lt. Freddy Cuela in Tacna said no damage or injuries were reported. Peru's navy tweeted a tsunami alert for the country's extreme southern coast, which is next to the Chilean region hit by the quakes.
Earlier, authorities reported just six deaths from Tuesday's magnitude-8.2 quake, but didn't rule out the possibility others could have been killed in older structures made of adobe in remote communities that weren't immediately accessible.
The tsunami after Tuesday night's quake caused the sea to rise only 8 feet (2.5 meters) in Iquique, a city of nearly 200,000 people, although that was enough to sink and damage many fishing boats. Iquique's fishermen poked through the wreckage Wednesday trying to assess what it will coast to repair and replace.
Still, as Bachelet deployed hundreds of anti-riot police and soldiers to prevent looting and round up escaped prisoners, it was clear the loss of life and property could have been much worse from Tuesday's powerful tremor.
Tuesday night's mandatory evacuation lasted 10 hours in Iquique and Arica, the cities closest to the epicenter, and kept 900,000 people out of their homes along Chile's coast. The order to leave was spread through cellphone text messages and Twitter, and reinforced by blaring sirens in neighborhoods where people regularly practice earthquake drills.
But the system has its shortcomings: The government has yet to install tsunami warning sirens in parts of Arica, leaving authorities to shout orders by megaphone. And less than 15 percent of Chileans have downloaded the smartphone application that can alert them to evacuation orders.
Chile is one of the world's most earthquake-prone countries, and tsunamis are a particular danger because of activity in the fault zone just offshore where the Nazca tectonic plate plunges beneath the South American plate.
Associated Press writers Eva Vergara in Santiago, Michael Warren in Buenos Aires, Argentina; Frank Bajak in Lima, Peru, and Andrew Dalton in Los Angeles contributed to this report.