The pilots were 45 minutes into a training mission Wednesday when the plane began to malfunction, said Col. John Hanna, operations group manager at the base.
The pilots arced the plane to help it lose momentum and minimize injury before they ejected, he added.
One pilot was uninjured but the second complained of back problems. Both were taken to a hospital as a precaution, Collin Williams, a spokesman for Rural/Metro Fire Department said.
No one on the ground was injured and no structures were damaged.
The Air Force has opened an investigation into the cause of the crash though results won't be released for another 90 days, The Arizona Republic reported Thursday.
All other flights at the base were suspended until investigators evaluate the fleet, the newspaper said.
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