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Aguirre has paid the price for his team's disastrous run of form that has seen them fail to win a game in 2009. During that time Atletico has been knocked out of the Kings Cup as well as falling from a top-four position in the Primera Liga, down to seventh in the table.
Atletico are now five points behind fourth placed Valencia and only three ahead of Athletic Club Bilbao, who beat them 3-2 in the Vicente Calderon Stadium three weeks ago.
Aguirre was in his third season as first team coach. The former Osasuna boss led his side to a fourth place finish least season and a subsequent place in the Champions League after defeating German outfit Schalke 04 in a qualifying play-off.
This season started with high hopes as Atletico kicked off their league campaign with a 4-0 win over Malaga. They may have lost in week two of the season, but another home win over Recreativo Huelva renewed hopes of a challenge for the Primera Liga title.
Nevertheless a 6-1 thrashing to FC Barcelona in the CampNouin October and a 2-1 home defeat to Real Madrid the following week, soon brought Atletico down to earth, although the club's solid campaign in Europe kept Aguirre free from criticism.
His side recovered to produce a nine-game unbeaten run in La Liga to end 2008 in third place in the table, all be it 10 points behind Barcelona. However, New Year defeats to Valencia and Athletic Club as well as a Kings Cup exit to Barcelona, saw them start to slide.
Atletico were poor as they lost 2-1 at home to Valladolid on Sunday and a section of the crowd called for both Aguirre's departure and that of club President Enrique Cerezo.
That was the final straw for Cerezo who announced Aguirre's departure on Tuesday. The new coach will be former Atletico goalkeeper Abel Resino, who was in charge at Second Division side Castellon.
"I am leaving with a clear conscience, I would never have expected this situation on December 20. But if we look at the results, we have fallen into a loosing streak and poor football, which obliged this decision to be taken," said Aguirre at the press conference to confirm his departure.