"An F16 combat aircraft crashed earlier today into the sea after its engine malfunctioned," he said.
Israeli media reports said the crash took place off the coast of the Gaza Strip Palestinian enclave.
"The pilot and navigator on board bailed out of their plane and were evacuated to a hospital," the army spokesman said, describing their condition as "stable".
According to the military, the two spent an hour in the sea before being pulled out by the air force's 669 rescue and evacuation unit.
Following the incident, air force chief Major General Amir Eshel "ordered all F16 and F15 aircraft grounded until the circumstances are reviewed," he said.
According to the military, it was the first time pilots had to bail out because of a malfunction since the Israeli military began using this model -- the F16-I -- in 1998.
In November 2010, two Israeli aircrew were killed when their US-manufactured F16 crashed during a training mission in the country's south.