The crossing, called Al-Qaa in Lebanon and Jussiyeh in Syria, was closed in 2012 as fighting raged between President Bashar al-Assad's forces and rebel fighters seeking his overthrow.
Assad's regime has since reclaimed most of the territory once held by the rebels, thanks to a Russian military campaign in support of his forces and deep divisions among the rebels.
Jihadists from the Islamic State group had moved into the border area but were pushed out in offensives by regime forces in Syria and the Lebanese army and militant group Hezbollah on the other side of the frontier.
It was the only one of the five crossings between Lebanon and Syria that was permanently closed by the war.
The head of Lebanon's General Security agency, Major General Abbas Ibrahim, said the re-opening of the crossing was a moment for celebration after it was closed by "terrorism that targeted the entire region".
The mainly Christian Al-Qaa area in Lebanon was targeted several times in cross-border attacks, including suicide bombings in June last year that killed five people.
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