In the audio message distributed online on Tuesday night, Abu Mohamed al-Jolani warned that Lebanon's Shiite Hezbollah movement would regret its intervention in the Syrian conflict in support of President Bashar al-Assad's regime.
"Our brothers in Qalamun are hiding plenty of surprises," Jolani said, referring to a mountainous region that runs along the Syria-Lebanon border.
"The real battle in Lebanon has yet to begin," he added, saying Hezbollah chief Hassan Nasrallah would "regret what he has done to Sunnis in Syria."
Hezbollah's decision to send fighters to bolster Assad's regime has drawn the ire of moderate and extremist groups in Syria alike.
Al-Nusra and other jihadist groups have actively targeted the group's strongholds in Lebanon in a series of bomb attacks that have killed dozens.
Signup to our newsletter and follow us on Facebook and Twitter!
Lebanon has seen the conflict next door spill over increasingly, with tensions rising between its Sunni community, which largely backs the Syrian uprising, and Shiites who back the Syrian government.
In addition to the bomb attacks, jihadist groups like Al-Nusra and the Islamic State group have battled Lebanese troops and Hezbollah forces along the border.
In August, fighters from the two jihadist groups briefly overran the Lebanese border town of Arsal, and they are still holding 27 Lebanese police and soldiers they took hostage, having executed three of them.
Nearly 190,000 people have been killed in Syria since the conflict erupted in March 2011.