The army said the operation near the border town of Arsal targeted an IS center. It said the local IS commander in the town, Ahmad Youssef Amoun, was captured after being seriously wounded. No troops were hurt, it said.
Hundreds of IS fighters are based in the area along the Lebanon-Syria border from where they launch attacks inside Lebanon.
Photographs said to be of Amoun and posted on local media websites showed a young man with a thick black beard lying on a hospital bed, a blood-stained white sheet covering most of his body.
"Such special operations strengthen stability and limit terrorist schemes," Aoun was quoted as saying.
The military said Amoun was behind several explosions that hit Lebanon recently, including the predominantly Shiite southern suburbs of Beirut, and took part in attacks against army positions in border areas.
IS has claimed responsibility for several explosions in Lebanon over the past two years that killed scores. The extremists have been holding nine Lebanese soldiers and policemen since a raid on Arsal in August 2014.
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