Jets fired three missiles at the Masnaa crossing, which lies about 300m beyond a Lebanese customs post.
The area is considered to be part of Lebanese territory.
Security officials said there were no casualties from the strike, which damaged two cars.
Police sealed off the area and prevented journalists from coming close.
They said the road between Syrian and Lebanese checkpoints was closed in both directions.
The passage has been an escape route for tens of thousands of Lebanese, who fled by land to Syria after Israel bombed Beirut airport in the first days of fighting.
It was also a gateway for humanitarian aid entering the country.