The 60-year-old former sprinter is taking over from fellow Frenchman Essar Gabriel, who stood down at the end of his term last October.
The International Association of Athletics Federations' deputy secretary general, Nick Davies, also stood down temporarily pending a review into allegations that he covered up Russian doping suspicions.
"Jean Gracia, who is a former general secretary of the French Federation and a current vice president of European Athletics, brings vast experience and will assist the continued smooth running of the association in the interim," IAAF president Sebastian Coe said.
"He will act as the focal point for all our member federations and partners, and support me with work involving the executive board and council."
The IAAF added that a permanent CEO/Secretary General, a new position, would be appointed "by the middle of the year".
An independent commission of the World Anti-Doping Agency (WADA) has stated in a damning report that "corruption was embedded" at the IAAF.
The report found that a clique run by former IAAF president Lamine Diack covered up organised doping and blackmailed athletes while senior officials looked the other way.
Diack is under formal investigation in France on suspicion of corruption and money-laundering linked to the concealment of positive drug tests in concert with Russian officials.
In November, following the publication of another WADA report, athletics superpower Russia were banned from competition for state-sponsored doping.
(Reporting by Julien Pretot, editing by Pritha Sarkar)
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