Lebanese police and Hezbollah say the captured men are civilians.
The five captives have been named as Bilal Nasrallah, his father Hasan Nasrallah, Muhammad Shukr, Ahmad al-Ghouta and Hasan al-Bourji.
An Israeli army spokeswoman said the men were brought to Israel. She said none of the soldiers who took part in the operation was injured.
They had landed by helicopter near the al-Hikmah hospital in Baalbek in the eastern Bekaa valley.
The Israeli raid came as its forces continued air strikes across South Lebanon.
Hezbollah fired a record number of rockets at Israel on Wednesday, with reports that it had hit central Israel for the first time.
At least 19 civilians, including a Syrian national, were killed and more than 20 wounded in air strikes near where the Baalbek operation took place.
At least 19 civilians were killed in
Security sources said jets bombarded the village of Jammaliyeh during clashes nearby between the commandos and Hezbollah, destroying several houses.
They said the seven members of a family were found dead in one house.
The toll was expected to rise when rescuers finished lifting the rubble of other houses.
Baalbek is about 100km north of the Litani River, which the Israelis have set as the northern boundary for their expanded ground operation announced on Tuesday.
Lebanese security officials have reported that more than 300 rockets were fired towards Israel by Hezbollah fighters on Wednesday.
Israeli police said more than 80 had landed in the north of the country, killing one person and wounding at least 19 people.
Israel Radio reported that one rocket hit the town of Beit Shean almost 70km from the border – the farthest inside Israel a rocket has struck. The army and police are checking the report.
The attack would mark the first time that Hezbollah has hit what is considered Israel’s central region, the country’s most populated area.
The heavy bombardment marked a step up in attacks after a two-day lull in activity by the Lebanese group.
Rockets fell on the tourist town of Tiberias, near the Sea of Galilee, as well as Kiryat Shmona, Nahariya and Safed.
Sirens also sounded in Haifa, Israel’s third-largest city, which lies about 35km from the Lebanese border, in anticipation of rocket strikes.
Two oil tankers are being allowed by Israel to sail into Lebanon to help ease a growing fuel crisis in the country.
The World Food Programme said it had negotiated safe passage for two shipments totalling 87,000 tonnes of oil and diesel to reach the ports of Beirut and Tripoli on Thursday.
Christiane Berthiaume, a spokeswoman, said: “The fuel situation is really critical across the country.
“Almost all the petrol stations are shut. Fuel supplies for power stations and water pumping stations are all but exhausted.”
Lebanese soldier killed
In a separate development, Israeli aircraft attacked a Lebanese army base in south Lebanon, killing one soldier and injuring two others.
The jets fired at least one missile at the base in the village of Sarba, in the Iqlim al Tuffah province, a highland region where Hezbollah is also believed to have offices and bases.
An official said the soldier was killed instantly.
It was not clear what prompted Wednesday’s attack on the base.
The casualties bring to 26 the number of Lebanese army soldiers killed in Israeli air strikes since the start of the offensive against Lebanon on July 12.