Ghana lost the final 11-10 on penalties to Cote d'Ivoire and although, both Abedi and Yeboah have previously denied their involvement in the defeat, the former Asante Kotoko star says they divided the players.
"Whoever will say the confusion between Abedi 'Pele' Ayew and Anthony Yeboah did not cost Ghana is lying," Gyan told Suncity Radio.
"It had a serious effect on the team because the players brought division in camp. If you ask Ayew or Yeboah, they will deny it but a third party like myself knows how we suffered.
"Players from Accra were in support of Ayew while those of us from Ashanti region, Brong Ahafo and Central region were behind Yeboah, so you can imagine the uneasiness at the camp. And that cost us the chance to win the Afcon trophy and even qualify for the 1994 Fifa World Cup in USA.
"Till date, some of the players are still at loggerheads with each other and I'm not even in good terms with Ayew despite starting my career with him at RTU," he added.
Gyan also believes the division currently exists in the Black Stars due to the presence of Ayew's two sons -Andre and Jordan.
"That type of division is still in the current Black Stars setup although Stephen Appiah tried to curb it when he was made the captain. But Asamoah Gyan has been unable to maintain that because of the presence of Andre and Jordan Ayew. The sons of Abedi are causing troubles just like their father," he said.
Ghana have reached the semifinals five consecutive times since 2008 but have failed to win the title on all occasions. The Black Stars will play Ethiopia in the 2019 Afcon qualifiers at the Baba Yara Sports Stadium on June 11.