Almeria held an emergency board meeting immediately after the match and Lillo was informed he had been fired before he left their Mediterranean Games stadium.
"The reason is purely sporting and comes after the bad results Almeria have suffered in recent weeks that have seen the side slip into the relegation places," said a club statement.
Lillo, 45, was under mounting pressure after a poor start to the campaign and the embarrassing loss to Barca left Almeria 18th in the 20-team standings with nine points from 12 matches.
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