The abduction of the teenagers was a trigger for the recent conflict in Gaza.
At first the military said it had only confirmed that one of the suspects had been killed and the other was also believed to dead.
Formal confirmation is expected after the secnd suspects’ body has been recovered.
Chief of Staff Lt Gen Benny Gantz said: "We promised the [teenagers'] families that we would find the murderers. This morning, we did just that.
"This isn't a consolation for the grieving families.
“But I hope that knowing we reached their children's murderers may slightly comfort them."
One of Mr Qawasmeh's relatives has already been charged with planning the teenagers' abduction.
The militant Islamist group Hamas originally denied being behind the killings but its political leader Khaled Meshaal later admitted its members had carried them out.
