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The ministry said the strikes targeted five locations in the southern regions of Tyre and Nabatieh, as well as the Bekaa region in eastern Lebanon.
It updated an earlier toll given by Lebanese official media which had reported two of the deaths in the south.
Lebanon's state-run National News Agency (NNA) reported the strike hit near the strategic Ali al-Taher ridge, which the Israeli army said it had captured, though Hezbollah did not confirm losing it.
Two young men were targeted while riding a motorcycle in the city of Nabatieh, NNA said, adding that rescuers transported their bodies to a local hospital.
Israel announced on Thursday it had taken control of the ridge. Defence Minister Israel Katz said the military would work to "prevent the enemy from re-establishing itself in the area".
Israel stepped up strikes in the Nabatieh region on Friday and also targeted the village of Rmadiyeh in the Tyre area, located more than 10 kilometres from the Israeli border.
The ministry said the third person was killed and 15 others hurt there, including two children, three women and six rescuers.
A rescue service source earlier told AFP that the strike in the village, which is sheltering people displaced from other southern areas, had hit a house.
Israel responded with airstrikes and a ground invasion that Lebanon says have killed more than 4,300 people.
The conflict has calmed since a US-Iran memorandum of understanding and a framework agreement between Israel and Lebanon was agreed in June, but Beirut still reports Israeli strikes.
Imran Riza, the UN humanitarian coordinator for Lebanon, said on X on Friday that families returning to Nabatieh following the truce "face widespread destruction, lack of basic services, ongoing insecurity and uncertainty".