Valparaiso, Aysen, and Magallanes were the only three regions out of 16 where candidates secured 40 percent of the votes needed to secure the governor's post in the election first round celebrated last month.
On Sunday, polling stations will be open from 8.00 am until 6.00 pm. The candidates would be those who obtained the first two places by votes in each region.
It is the first time that Chileans elect governors' posts because the position was determined by the President.
Subnational elections are taking place amid a pressing COVID-19 situation, especially in the Metropolitan Region which is the most important governorships at stake. As of Saturday morning, health authorities had reported 1,468,992 COVID-19 cases and 30,579 related deaths.
"It is assumed that we should have a turnout below 43 percent recorded in the subnational election first round...the ghost of a structural abstentionism could reappear," Central University professor Marco Moreno said.
Besides electing the governors' posts, Chileans voted for 354 mayors, 2.252 councilors, and 155 representatives of the Constituent Convention on May 15 and 16.