Brigadier General Mohammed Sleiman was shot in the head and neck on August 1, 2008 by a small team of Israeli commandos as he enjoyed a dinner party at his luxury seaside home on the Syrian coast, said The Intercept website, citing the leaked files.
The Israeli military team then escaped by sea.
"The internal National Security Agency document, provided by former NSA contractor Edward Snowden, is the first official confirmation that the assassination of Sleiman was an Israeli military operation," said the website.
The revelation "ends speculation that an internal dispute within the Syrian government led to his death," it added.
The NSA's internal version of Wikipedia, "Intellipedia," described the assassination near the port town of Tartus as the "first known instance of Israel targeting a legitimate government official," according to The Intercept.
It cited three former US intelligence officers as saying that the document's classification markings indicated that the NSA learned of the assassination through surveillance.