"Ghfran Almouhamad, 23, provided a urine sample on 3 August 2012 in London that indicated the presence of methylhexaneamine. The analysis of the B sample confirmed the results of the A sample," the International Olympic Committee said in a statement.
She had placed eighth in the second heat of the first round on August 5.
"The International Association of Athletics Federations is requested to modify the results of the above-mentioned event accordingly and to consider any further action within its own competence," the IOC added.
She now faces a maximum two-year ban as a first-time offender.
Syria has sent 10 athletes to the Games despite a 17-month-long bloody uprising against President Bashar al-Assad's rule.
The hurdler is the 11th athlete to be eliminated from the Games either by the IOC or by a national team since the start of the Olympic period on July 16.
Methylhexaneamine was first placed on the World Anti Doping Agency's Prohibited List in 2010 and is banned only in competition.
The substance can be found in nutritional supplements, typically those designed to increase energy or boost weight loss and in nasal decongestants.
The IOC will run more than 5,000 tests at the Games that end on Sunday.
More than 100 athletes were also caught using banned substances in the months leading up to the Games following increased testing by national and international anti-doping agencies, designed to root out cheats before they arrived in London.