Staff at a US Air Force base in South Carolina had called for the public's help in locating the jet - or its remains, Sky News reports.
The Marine Corps pilot safely ejected over North Charleston on Sunday afternoon - and was taken to hospital after parachuting to the ground.
Military spokesperson Major Melanie Salinas said he was in a stable condition.
The plane was eventually located in a rural part of Williamsburg County, about two hours northeast of the base in Charleston.
Residents were being asked to avoid the area while a recovery team worked to secure it.
"We are transferring incident command to the USMC this evening, as they begin the recovery process," the base posted on X (formerly Twitter).
In a post on Facebook, Joint Base Charleston said: "The public is asked to cooperate with military and civilian authorities as the effort continues."
It described the incident as a "mishap" and called for anyone with information that could assist "recovery teams" in their search to get in touch.
Police helicopters took part in searches over Lake Moultrie and Lake Marion after bad weather cleared.
Officials are investigating why the pilot was ejected.
The planes and pilots were with the Marine Fighter Attack Training Squadron 501 based in Beaufort, not far from South Carolina's Atlantic coast.
RHM/PR