The Turkish presidency's failure to place a chair for von der Leyen alongside President Recep Tayyip Erdogan and EU Council chief Charles Michel was "an insult from Turkey," Beaune said on RTL television.
"Turkey behaved badly," he added, calling it "a Turkish problem done deliberately towards us... we shouldn't be stirring up guilt among Europeans".
Von der Leyen's being shunted aside prompted recriminations from European capitals to Turkey, but also within Brussels.
For its part, Ankara insists the incident was down to tangled wires between the Council and Commission, separate EU institutions.
Michel's staff claimed they had no access to the meeting room before the Tuesday event, but also highlighted that the Council chief comes before the Commission president under strict international protocol.
"It was a kind of trap... between the one who laid it and the one who walked into it, I'd rather place the blame on the one who laid it," France's Beaune said.
Echoing Italian Prime Minister Mario Draghi, who called Erdogan a "dictator" in response to the sofa incident, Beaune charged that there was "a real problem with lack of respect for democracy and an autocratic drift in Turkey" that should prompt Europeans to be "very firm with the Turks".
Nevertheless, "in future, it would be good if there was one single presidency of the European executive," Beaune acknowledged.
"We need stronger European institutions".
Reporter's code: 50101