The pilot was conducting routine flight operations when the crash happened. They safely ejected and were recovered by a military helicopter, Pacific Fleet said. The pilot is in stable condition.
Six others were injured on the deck of the carrier. Three required evacuation to a medical facility in Manila, Philippines, where they are in stable condition, according to Pacific Fleet. The other three sailors were treated on the carrier and have been released.
The cause of what the statement called a "inflight mishap" is under investigation.
A spokesman for the Navy's 7th Fleet in Japan, Lt. Mark Langford, said Tuesday the impact to the Vinson's flight deck was "superficial" and the warship and its air wing had resumed normal operations.
As for the F-35, "the status of the recovery is in progress," Langford said.
The crash is the first for an F-35C, the US Navy's variant of the single-engine stealth fighter, designed for operations off aircraft carriers.
The F-35A, flown by the Air Force, takes off and lands on conventional runways, and the F-35B, the Marine Corps version, is a short-takeoff vertical landing aircraft that can operate off the Navy's amphibious assault ships.
Versions of the F-35 are also flown by US allies and partners, including Japan, South Korea, the United Kingdom, Australia, Italy, Norway, the Netherlands and Israel. More countries have orders in for the jet.