Wadephul, the first European foreign minister to journey to Israel since the war with Iran began on February 28, met his Israeli counterpart Gideon Saar for talks in Jerusalem.
After boarding his military plane to depart Tel Aviv, alarms sounded amid a new Iranian attack on Israel.
The minister and accompanying officials were forced to leave the plane and head to a protective bunker.
Following the all-clear, Wadephul said, "Everything's fine here!" and gave a thumbs-up.
The Ynet news portal reported that Beit Shemesh was hit by missile debris, hours after Wadephul and Saar visited the city west of Jerusalem where nine people killed and 50 injured in an Iranian missile attack on March 1.
In total, there have been 13 deaths in Israel as a result of Iranian attacks since the war began with the large-scale US-Israeli offensive against Iran.
Wadephul's visit came off the back of discussions with his Cypriot counterpart Konstantinos Kombos in Nicosia earlier on Tuesday.
Germany has largely backed Israel and the United States over the conflict with Iran but Chancellor Friedrich Merz said on Tuesday he was concerned that the countries lack a plan to end the war.
German officials are concerned about the sharp rise in fuel prices as a result of the war, which could have a devastating effect on economic growth.
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