Kerry made the announcement on Monday shortly after the Syrian conflict marked its three-year anniversary this weekend.
Rubinstein succeeds Robert Ford in the job. Ford, a veteran diplomat, retired earlier this year amid a breakdown in talks between the Syrian government and opposition forces.
Ford has been ambassador to Syria since January 2011, but has not lived in Damascus since February 2012, when the State Department suspended embassy operations there.
According to reports Ford played a central role in laying the groundwork for the development of an armed insurgency directed against as the government of Syrian President Bashar al Assad.
Like Ford, Rubinstein speaks fluent Arabic and has served in numerous positions at embassies around the Mideast, including in Israel, Jordan, Iraq, Tunisia and Syria.
Kerry says Rubinstein will travel to the region in the coming week.
RA/NJF