An important route, Lincoln Boulevard, was closed during the early morning commute because of the fire and re-opened at 11 a.m.
The San Francisco National Cemetery was closed to the public so that firefighters could clean up the mess and reopened at 4 p.m.
The fast-moving brushfire broke out inside the Presidio and was a challenge for firefighters as it burned through a eucalyptus grove. Getting into the grove was tough and water had to be trucked in because there were no hydrants nearby.
The fire was out by sunrise. However, plenty of hotspots remained and one thing became very clear - just how close the fire came to the national cemetery.
"Our first concern is our residents and tenants here in the Presidio, but we do have a lot of historic and national resources that we're worried about as well," Presidio Trust spokesperson Dana Polk said.
Some of these gravesites date back to the Civil War.
"The cemetery is sacred ground." Presidio resident Emerson Johnson said.
He lives in the Presidio and was relieved the headstones were saved.
"Just to walk through and read the headstones and see the sacrifices that have been made for us to live the life we do," Johnson said.
"So we'll probably talk about the fire this morning and what happens to the trees," Summer camp owner Linda Constant said.
She leads nature walks through the same grove which burned.
"I wondered what may have started it. I do know that there some little encampments here and there that we'll find when we're out and about in the forest of people are sleeping," Constant said.
Crews say they didn't see any homeless camps around the scene of the fire. The fire did not threaten any homes and did not damage any of the historic gravesites.
Firefighters are investigating the cause of the fire and told ABC7 News that a brush fire inside the Presidio could be a first because the fog keeps things so damp.