"Atalanta communicate that they have accepted the resignation given today by Mr. Antonio Conte," the Bergamo club said on their website.
Academy coach Valter Bonacina would take charge of Thursday's training ahead of Sunday's visit to Palermo, the club added.
Conte, who led Bari to promotion from Serie B last term but left the southerners before this season started after a disagreement over transfer targets, replaced Angelo Gregucci in September after Atalanta lost their first four matches.
The Bergamo club, who are usually mid-table, were unbeaten in their first five league games under former Italy and Juventus midfielder Conte but their recent form has been poor and fans called for his head after Wednesday's 2-0 home defeat by Napoli.
Italian media said former Atalanta coaches Nedo Sonetti and Bortolo Mutti were among the favourites to replace Conte.
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