Andrea Tenenti says the UN is looking into the circumstances of the incident.
He did not disclose the nationality of the soldier, but local media reports said he was a Spanish national.
The UN peacekeeping force known as UNIFIL has been deployed in south Lebanon since 1978.
The Lebanese Hezbollah group claimed responsibility for firing a missile that hit an Israeli military convoy earlier today, prompting an apparent retaliation from Israel, which fired at least 50 artillery shells into Lebanon in a significant escalation along the volatile border.