Ahmad Al Salih headed the winning goal for Syria's Red Eagles in the 75th minute of the final and they rode their luck in the closing stages before claiming the nine-team biennial tournament.
"I give this win and this worthy title to the Syrian people.
I thank God that we succeeded in bringing happiness to the sad people," striker Omar Al Soma said.
More than 40,000 people have been killed in Syria since violence broke out against the rule of President Bashar al-Assad in March 2011.
The Syrians reached the final after drawing with Iraq and coming from behind to beat Jordan in the group stages. They then edging Bahrain 3-2 on penalties when their semi-final finished 1-1 after extra time.
They had twice previously finished as runners-up in the tournament, in the inaugural edition in 2000 and again four years later, both times losing to Iran.
Syria are ranked 144th by FIFA and have never qualified for a World Cup but have made the Asian Cup finals on five occasions, most recently last year.
They begin the qualifiers for the 2015 Asian Cup in February and will play home matches against Singapore, Jordan and Oman in Iran. The top two teams from the group will compete in the finals in Australia.