The IOC said in a statement that Fazekas had refused to provide a complete urine sample after Monday's final, which qualified as a serious anti-doping violation.
He has been ordered to return his gold, the IOC said.
Lithuanian Virgilijus Alekna will now be awarded the gold, Zoltan Kovago of Hungary and Aleksander Tammert of Estonia the bronze.
Fazekas is the second athletics gold medallist to forfeit his title at the Athens Games after a positive test.
Irina Korzhanenko of Russia was stripped of her women's Olympic shot put gold on Sunday after testing positive for a steroid.
An IOC source said earlier Belarussian high jumper Aleksey Lesnichiy, who was last in the qualifying round, had tested positive for the anabolic agent clenbuterol.
Officials at the Belarussian Olympic Committee in Athens said they were unaware of any failed dope test involving their athlete.
