Air force commander Maj. Gen. Amir Eshel ordered an investigation and grounded the Cobra fleet until the circumstances of the crash are clarified.
The two pilots were identified as Lt. Col. Noam Ron, 49, and Maj. Erez Flekser, 31, the army said.
The pilots were on a routine training flight to the Palmachim Air Base when contact was lost about 1 a.m. The wreckage was found some four hours later not far from Kibbutz Revadim.
The last air force accident involving Cobra helicopters was in September 2008 when two pilots were killed after crashing in the Galilee, The Jerusalem Post said.