Colantuono - who helped Atalanta back into the top flight during 2010-11 - leaves the club three points off the relegation zone having won just five times in the league all season.
After five years with the club, the 52-year-old is replaced by Reja, who had been out of work since leaving Lazio in June.
Reja's first game in charge comes on Sunday when Atalanta are due to face financially-troubled Parma at Stadio Ennio Tardini.
"Atalanta B.C. communicate that they have dismissed coach Stefano Colantuono, who will be replaced by Mr Edy Reja," read a statement on Atalanta's website.
"The club expresses profound appreication and gratitude to Mr Colantuono on account of the work he has done over the past five years."
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