"We see Hamas as responsible for the kidnapping and the murder, and we know how to settle accounts with them," Ya'alon warned, reiterating comments made by Prime Minister Binyamin Netanyahu on Monday night.
Ya'alon suggested that the West Bank operation, which has included hundreds of arrests of Hamas operatives in the West Bank over the past two-and-a-half weeks would continue.
"We will continue to hunt down the boys' murderers, and we will not rest nor remain silent until we get our hands on them," the defense minister vowed.
Ya'alon sent condolences to the families of Gil-Ad Shaer,16, Eyal Yifrah, 19, and Naftali Fraenkel, saying that "the heavy sorrow which envelops you, envelops the entire nation."
He praised the parents of the boys for their strength in dealing with the kidnappings, "which granted the IDF, the Shin Bet (Israel Security Agency) and the Israel Police the strength to continue the search until its bitter end."
Ya'alon also praised the security forces involved in Operation Brother's Keeper for their "impressive demonstration of cooperation and their sense of mission."
The two suspects whose names have been released by authorities - Marwan Kawasme, 29, and Amar Abu Aysha, 32, - remain at large.
IDF forces raided the homes of Kawasame and Abu Aysha, known Hamas operatives from the Hebron area, early Tuesday morning after the bodies of the Israeli teens were discovered.
As security forces intensify the search for the two suspects, large numbers of troops have converged on Hebron and the Beit Khalil region, closing off the area.