The 62-year-old Culpi took over at Atletico for a fourth time in April 2014 and helped the club to the Recopa Sul-Americana, the Brazilian Cup and the Minas Gerais state championship.
They are currently in second place in the league table with two games remaining, they have a guaranteed place in next year's Libertadores Cup but Culpi told reporters on Thursday: "We've come to the end of a cycle.
"I could have continued for two more games but the directors opted to end this period. I think it is important to start planning for 2016. This is a very sad day for me."
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With just two weeks left, Culpi's departure means that champions Corinthians are set to be the only club to start and finish the season with the same coach, 54-year-old Tite.
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