Hassan Nasrallah, in a televised speech, said the battle in the mountainous area was "ongoing in terms of time and place," but that Hezbollah had dealt "resounding defeats" to rebels there.
Hezbollah and the Syrian regime have "kicked out the armed groups from the battlefield, retaking control of 300 kilometres (nearly 200 miles) of territory," Nasrallah said.
He dismissed reports that Hezbollah had lost dozens of fighters in the battle, saying 13 had been killed.
The Qalamun region straddles the Syria-Lebanon border and was a stronghold of rebel forces until a major operation by Syrian regime troops backed by Hezbollah fighters last year.
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While most of the region was recaptured, opposition militants and jihadists remain entrenched in the area along the porous and ill-defined border.
From there, jihadists have launched attacks inside Lebanon, including in August 2014 when fighters from Al-Qaeda's Syria affiliate Al-Nusra Front and the Islamic State group briefly overran the eastern Lebanese town of Arsal.
As they withdrew from Arsal, the groups took several dozen Lebanese security forces with them as hostages and remained hidden in the town's outskirts.
"As long as the armed groups are present in Arsal's outskirts and in the remaining parts of Qalamun... we cannot talk about full security," Nasrallah said.
He said Hezbollah was fighting "from hill to hill, from valley to valley" to push back armed groups, and that Lebanese border villages were safer as a result.