Cooler conditions and lighter winds aided fire crews as dawn broke but South Australia state Premier Jay Weatherill said it would be days before the situation was brought under control.
"Even though a significant proportion of the fire perimeter is under control and the conditions were milder overnight many fire fronts are still active within the fire grounds and they'll continue to be battled for some days," he said.
"Obviously we have had the awful news of the tragic death of at least two people and we hold grave fears for many more," Weatherill said.
"We can't be entirely sure that we have identified every single person within the fire ground. That work will continue this morning as we carry out a more detailed search of the fire area."
He added that 13 people were in hospital with five in either a critical or serious condition with significant burns.
The blaze incinerated at least 16 homes, as well as outbuildings, farm machinery and vehicles as it raged across a 40-kilometre front, driven by strong, swirling winds late Wednesday, he added.
Livestock was also lost with reports that 2,000 pigs were killed along with up to 150,000 chickens.
Country Fire Service chief officer Greg Nettleton said it might still be early in the fire season but the land in South Australia was incredibly dry and only long, soaking rain would cut the fire risk.
