Chief of Staff Gadi Eisenkot, speaking to a security conference, said intelligence had led Israel to the conclusion and matched previous reports.
Hezbollah itself has said Mustafa Badreddine, who was on a US terror sanctions blacklist and wanted by Israel, was killed in an explosion in May 2016 near Damascus international airport.
A probe had concluded that Sunni Islamist radicals known as "takfiris", who consider Shiites to be heretics, had killed Badreddine, according to Hezbollah.
"Those findings show to what degree relations between Hezbollah and its patron Iran are tense and complex," he said.
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Hezbollah has deployed thousands of fighters in Syria, where Badreddine had led its intervention in support of President Bashar al-Assad's forces, which are also backed by Russia and Iran.
The Shiite movement has said Badreddine was killed by artillery bombardment of one of its positions near Damascus airport.
It did not name any specific Islamist group, and there has been no claim of responsibility for the killing.
Badreddine was a key suspect in the 2005 assassination in Beirut of Lebanese ex-premier Rafiq Hariri.
Israel considers Hezbollah among its top threats and fought a devastating 2006 war against it.
Its military believes Hezbollah has between 100,000 and 120,000 short- and medium-range missiles and rockets, as well as several hundred long-range missiles, with the medium-range missiles capable of reaching Tel Aviv.
Israeli military officials have said regularly in recent months that they will respond with heavy force against Lebanon if Hezbollah were to attack from there.
However, many analysts say the Lebanese militia's involvement in Syria has made another conflict with Israel less likely for now.
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