A senior security official told AFP on Sunday: "The 'military lane' was permanently closed last night and we shall issue an official statement on that matter.
"Actually, since October the lane had been cancelled except for military logistics, military officials on an official mission and the head of the Lebanese-Syrian Higher Council. Even ministers and MPs were not using it any more.
"Now all those who want to go to Syria will have to go through the official borders manned by general security."
The closure comes amid tension between the two neighbours after the murder in Lebanon on Monday of Jebran Tueni, a prominent anti-Syrian journalist and politician.
Anger has been rising in Lebanon over a series of assassinations, widely blamed on Syria but denied by Damascus, since the murder in February of Rafiq al-Hariri, the former Lebanese prime minister.
The special crossing, parallel to the main Masnaa border point in eastern Lebanon, was mainly used by Syrians and their Lebanese allies as well as prominent business people from the two countries.
During its 29-year military presence in Lebanon that ended last April, Syria distributed to its Lebanese allies "special permits" for the crossing.
The system was often criticised for encouraging corruption and illegal activities.
The annual VIP permits were issued to Syrian and Lebanese politicians, security officials and business people free of charge for some and costing up to about $2000 for others.
The permits allowed holders to cross without customs or other formalities.
All Syrian and Lebanese nationals are allowed visa-free visits to each other's countries.