More strong winds were forecast to whip across the state and neighboring New Mexico.
Flames from the blaze raced through rural communities near Flagstaff days earlier until Thursday's break in the weather allowed authorities to survey the damage and permitted helicopters to drop water for the first time.
Thirty homes and numerous other buildings are destroyed and authorities said more than 100 properties were affected.
The U.S. Forest Service in the Coconino National Forest reported Friday that the Tunnel Fire was 3% contained, spanning 21,087 acres.
"Though welcome rain fell this morning across many parts of the fire, strong winds forecast today and shifting winds out of the north and east forecast for Saturday and Sunday are still a major concern for fire managers," the agency said.
It has burned close to 32 square miles and forced the evacuations of approximately 765 homes and 1,000 animals since it broke out on Sunday.
There are more than 370 firefighters on scene, nine 20-person hand crews, five dozers, 30 engines, one air attack plane, two Type 1 helicopters and one Type 3 helicopter.
The Coconino National Forest has instituted a forest closure order for the area affected by the Tunnel Fire. U.S. Highway 89 remains closed from near milepost 425 to 445.
On Thursday, Gov. Doug Ducey declared a state of emergency for Coconino County "to assist impacted communities with the resources needed to respond to and recover from the fire’s destruction."
The cause of the fire is still under investigation.
The National Interagency Fire Center said that 12 large fires have scorched more than 67,000 acres in the Southwest, Southern and Alaska areas.
Wildfire has become a year-round threat in the West. Scientists have said that problems have been exacerbated by decades of fire suppression and poor management along with a more than 20-year megadrought that studies link to human-caused climate change.
The Associated Press contributed to this report.