Cmdr. Greg Hicks of the U.S. Navy's 3rd Fleet said the accident happened on a road in the southwest part of the base, the San Diego Union Tribune reported Tuesday.
The truck the three sailors were riding in was carrying drinking water to re-supply a campsite taking part in a joint Navy-Marine Corps exercise when the rollover occurred.
Hicks said he did not know if rainy conditions Monday when the accident occurred were a contributing factor.
Two of the sailors were pronounced dead at the scene while a third sailor was airlifted to a hospital in stable condition, The Orange County (Calif.) Register reported.
All three sailors were part of Amphibious Construction Battalion One.
The names of the victims have not been released.