The USAF did not disclose the pilot's name, but said he is in stable condition after being admitted to a hospital on the base for observation.
The crash of the $150 million aircraft occurred about 12 miles (19 kilometres) northeast of Eglin on the base's test and training range, the Air Force said in a statement.
"There was no loss of life or civilian property damage related to the crash," it said.
An investigation will be launched into the crash.
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