The toll was revised down by Pakistan's Provincial Disaster Management Authority from 20 dead and more than 300 injured.
The USGS initially measured the quake at 5.7 magnitude, but revised it to 5.9 a few hours later. It also revised the depth from 20.8 kilometers (12.9 miles) to 9 kilometers (5.6 miles).
The quake caused power outages and damage across Harnai, according to resident Zafar Khan Tareen. The district consists of numerous scattered villages of basic mud houses that are home to coal mining communities.
"We went out and took our children out at the same time. Thank God everyone in our house is safe. However, the roof and walls of the house were badly damaged," he said.
"Almost all the shops have also collapsed and in every street of villages ... one or two people have died and many children are among the injured."
Harnai resident Muhammad Ali said his daughter was killed when a room in his house collapsed. The other rooms were also badly damaged, with cracks in the walls, he said.
"When the earthquake occurred last night, many people ran out of their houses. We also ran out but one of my daughters died, two other girls were left behind and are injured," he said.
In a Twitter post Thursday, Pakistani Prime Minister Imran Khan expressed his sorrow at the loss of lives in the earthquake.
"I have ordered immediate assistance on an emergency basis for the Harnai, Balochistan, earthquake victims & for an immediate assessment of the damage for timely relief & compensation. My condolences & prayers go to the families who lost their loved ones," he wrote.
Sohail Afridi, the district commissioner of Harnai, said rescue efforts were ongoing.
"Since 3 a.m. the rescue operation has been underway. The injured have been taken to the hospital via helicopter," Afridi said, adding the situation is "currently under control."
Harnai's rural location makes it difficult to access, welfare organization Edhi Foundation told CNN.
CNN's Sophia Saifi reported from Karachi and Azaz Syed reported from Islamabad.