No new major damage or casualties were reported after the 7.6-magnitude aftershock, which struck just before midnight local time.
Chile's Emergency Office and navy issued a tsunami alert and ordered a precautionary evacuation of low-lying areas of the country's 2500-mile Pacific coastline.
Among those moved inland was President Michelle Bachelet, who was in the city of Arica assessing damage in the north from the initial earthquake.
She tweeted: "I was evacuated like all citizens. One can see that the people are prepared."
The evacuation order initially applied to the full coast, but authorities quickly lifted the alert for all but the far northern shore.
The whole coast was evacuated for several hours after Tuesday's earthquake, and for the night in the north, although the tsunami proved small.
Yesterday's aftershock caused buildings to shake and people to run out into the streets in the port of Iquique, one of the cities that suffered damage in the earlier earthquake.
The aftershock caused some landslides near Alto Hospicio near Iquique where about 2500 homes were damaged by the first earthquake.
The Ministry of Education again suspended classes in schools in the north. The aftershock was felt across the border in southern Peru.