The Ghanaian midfielder failed to make an appearance in the game as Diego Simeone opted for a midfield quartet of Koke, Rodri, Saul and Thomas Lemar.
Eibar looked to have snatched all three points when Sergi Enrich scored in the 87th minute to break the deadlock.
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But the Rojiblancos fought back and got an equalizer at the death through substitute Borja Garces Moreno to ensure both teams shared the spoils.
That result leaves Atletico in 10th places on five points with Barcelona and Real both in action later on Saturday.