The latest deaths bring the official toll from the temblors to about 550. The unofficial figure is as high as 700, with more than 800 injured.
People ran into the streets in panic after the aftershock, which had its epicentre in the impoverished Balochistan province.
Eight persons were killed in Nok Jo, a small village in Awaran with a population of around 15,000. Four more deaths were reported from Mashkay area, officials said.
Pakistan's met office said the aftershock measured 7.2 on the Richter scale. However, the US Geological Survey put the magnitude at 6.8 and said the epicentre was located 96 km northeast of Awaran district, which recorded over 300 deaths after Tuesday's temblor.
Over 60 mud houses collapsed when the aftershock struck, , said Deputy Commissioner Rasheed Baloch. The bodies of four persons killed by the earlier quake were also pulled out of the rubble, reports said.
"Poor communication system are a major hindrance in the relief operations," he said.
Strong tremors were felt in several parts of Balochistan. A session of the provincial assembly was underway when the the aftershock struck. Footage on television showed ministers and lawmakers walking out of the assembly as the session was hurriedly suspended.
