The Cameroon international has a "minor knee irritation", while Belgium winger Hazard travelled with the rest of the squad to Spain despite missing the last two games with a calf problem, the club said on their website.
Hazard picked up a calf injury in the early stages of Chelsea's second-leg victory over Paris Saint Germain on April 8 and has not figured in the Premier League for the Blues since.
Eto'o's absence means former Atletico captain Fernando Torres, Demba Ba or Andre Schuerrle are likely to get the nod from manager Jose Mourinho who also spent time in Spain as coach of Atletico's city rivals Real.
Mourinho's record in nine games against Atletico over three seasons with Real was eight wins and one defeat, the only reverse coming in last season's Copa del Rey final.
He hinted that Torres could start against his old club, even though he still counted himself as an Atletico supporter.
"Of course no team arrives in a Champions League semi-final without being a very good team," Mourinho said. "And they (Atletico) are no exception so to be here they have to be a very good team.
"Playing in the Champions League is a big motivation for every player. I am not saying that Fernando Torres will start, I am saying that he never hides. We feel that every day.
"He is a real Atletico supporter, I would say a big one. We talk about Spanish football every day.
"But he is a professional. I have no doubts that the minutes he will be on the pitch tomorrow he will do everything for Chelsea given the professional that he is."
The return leg is in London next week and the winners of the tie will play holders Bayern Munich or Real Madrid in the final in Lisbon on May 24.
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