The news of Ronaldo's absence from the game is a recent development, with no news outlet reporting that the Portuguese striker had a muscular problem.
However Juve boss Pirlo confirmed that Ronaldo is out of the game.
"Ronaldo won't be involved in the match. He has not recovered from a muscle problem, playing him tomorrow would have risked a major injury," said Pirlo in his pre-game press conference.
"Air travel, late matches and the accumulation of many matches haven't allowed him to recover. We preferred to let him rest and hope to recover him by Wednesday."
Pirlo has also confirmed that Paulo Dybala will start from the off against Atalanta. Dybala has missed the majority of the season through injury, limiting the 27-year-old to just 18 games in all competitions.
Pirlo is likely to utilise the same defensive back line that he deployed in last weekend's 3-1 win against Genoa.
Juan Cuadrado, Giorgio Chiellini, Matthijs de Ligt and Danilo will all occupy their positions in defence.
In midfield, Pirlo is expected to keep the majority of the same midfielders, with the notable exception of Dejan Kulusevski. The Swede will be replaced by American Weston McKennie on the left-hand side of a midfield four.
He will be joined by Federico Chiesa, Rodrigo Bentancur and Adrien Rabiot.
With Ronaldo's absence confirmed, Dybala will play alongside Alvaro Morata in attack for the Bianconeri.