The 18-year-old, who also competed in the 1,500 metres, won the steeplechase event on Sunday but EOC said her urine sample contained osterine, a banned substance.
"Ms Beji was therefore charged with an Anti-Doping Rule Violation," the governing body said in a statement on Saturday.
"It was determined by the EOC Executive Committee on the recommendation of the EOC’s Committee for Legal, Eligibility, Disciplinary and Doping Matters that she is suspended from participation in the European Games and that she is disqualified from the 3,000m steeplechase which took place on 21 June.
"Further anti-doping procedures will be conducted by the competent international organisations."
Hosts Azerbaijan finished fifth in the team athletics championship, narrowly missing out on promotion to the second tier of the European Athletics Team Championship.
Earlier in the inaugural games in the Azeri capital of Baku, 19-year-old Albanian boxer Rexhildo Zeneli was suspended after testing positive for another prohibited substance furosemide.
(Editing by Amlan Chakraborty)
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