Videos showed flames rising from the building as firefighters laboured through the night to stop the blaze, which started on Saturday night, from spreading in the dense business district.
After fighting the flames for over 24 hours, firefighters began cooling the steaming rubble of the nearly collapsed structure.
Firefighters told Pakistan's local television station Geo News that the lack of ventilation in the mall, which houses over 1200 shops, caused the building to fill with smoke and slowed rescue efforts.
"It appears to have been caused by a circuit breaker," Sindh police chief Javed Alam Odho told reporters at the site on Sunday, according to Dawn News.
"The layout and construction of this market was such, and secondly, the nature of the items in it - such as carpets, blankets and other objects made of resins - so the fire is still simmering because of these."
Karachi Mayor Murtaza Wahab told reporters that 65 people were still missing.
Rescue officials said six people had been killed and 20 others were wounded.
According to media reports, people chanted slogans criticising the mayor who came to the site after 23 hours.
Hundreds of people had gathered around the building, including distraught store owners whose businesses had turned to ash.
"We've been left high and dry, reduced to zero; 20 years of hard work, all gone," shop owner Yasmeen Bano said.
The fire erupted on Saturday night, with rescue services receiving a call that ground-floor shops at the multi-storey Gul Plaza shopping centre were ablaze.
"When we arrived, the fire from the ground floor had spread to the upper floors, and almost the entire building was already engulfed in flames," Rescue 1122 spokesperson Hassanul Haseeb Khan told Reuters.
Images of the mall's interior revealed the charred remains of stores and a bright orange glow as flames continued to rise throughout the building.
