Manzano becomes the fourth coach in Spain's top flight to lose his job this season, following Michael Laudrup of Mallorca, Hector Cuper in Racing Santander and Juan Carlos Garrido, who was sacked by Villarreal on Wednesday night.
The former Mallorca, Rayo Vallecano, Malaga and Valladolid coach has lasted less than half of the season in what was his second spell at the club.
Manzano's agent, Garcia-Quilon, had confirmed to sports paper Marca earlier in the day that Atletico had called him with a view to rescinding Manzano's contract with the club's disappointing start to the campaign.
Manzano finally lost his job after Atletico were knocked out of the Copa del Rey by third tier side Albacete following a 0-1 defeat in the Vicente Calderon less than 24 hours earlier, Xinhua reported.
Manzano accepted an offer this summer to return for a second spell at the Vicente Calderon Stadium, but was never popular with the majority of fans, after his previous season in charge had ended with the club failing to qualify for Europe in 2004.
The coach did take Atletico into the last 32 of the Europa League, but their form in the domestic La Liga has been very erratic with their away form especially being a problem. Atletico have only managed to draw one game away from home and have not won in the league away from the Calderon.
Manzano also angered supporters by falling out with popular winger, Jose Antonio Reyes, who has not played in recent matches, despite being the club's most in-form player.
His position became increasingly uncomfortable a fortnight away as his side was beaten 2-1 by Albacete in the first leg of their Copa del Rey tie and following that a 4-2 thrashing away to Espanyol and a 2-0 home defeat to Betis.
Former Atletico player and Argentina international, Diego Simeone is expected to be named as Manzano's replacement.
Atletico confirm coach Gregorio Manzano's sacking
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