We use 13C/12C ratios of any produced metabolite to differentiate between biogenic and fossil carbon source all the time.  Assuming your "synthetic" ethanol came from a fossil source and you are fermenting sugar as opposed to fossil derived syngas, then 13C/12C ratio should work well.  

Delta carbon ratios are very accurate for identifying the differences between sources of granulated sugar by either sugarcane C4 and sugar beet C3 plants . Therefore, delta C differences for 100% ethanol at ratios of 10 to 20 percent ethanol in octane fuel should clearly separate ethanol fermented from both C3 and C4 plants and petroleum sources.

Sure, with 13C/12C ratios of ethanol you can descriminate between fermented and synthetically produced. It is possible to perfom a 13C/12C with 2H/H  analysis to discriminate between fermented and synthetically ethanol. [There are nine sample of ethanol from different botanical or synthetic origin: Anal. Chem., vol. 63, 1991, 2306-3313].