The European Commission and European Union Aviation Safety Agency (EASA) warned in a statement of "an overall intensification of air strikes and degradation in the security situation".
They issued an official recommendation "not to operate within the airspaces of Lebanon and Israel at all flight levels".
Provisionally lasting until October 31, the Conflict Zone Information Bulletin (CZIB) "can be reviewed earlier and adapted or withdrawn", the statement added.
"EASA will continue to closely monitor the situation, with a view to assess whether there is an increase or decrease of risks for EU aircraft operators as a result of the evolution of the threat," the body said.
Israeli bombardment of the southern outskirts of Beirut on Friday hit its highest intensity since the state's last war with Hezbollah in 2006.
The Israeli army claimed to have killed Hezbollah leader Hassan Nasrallah in an air strike, while the Iran-backed group said it had fired rockets towards a kibbutz and military targets in northern Israel.
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