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."
‘I don’t think Liverpool would look at Ollie Watkins, a striker isn’t a pressing issue for them – it’s Arsenal who need one’ Former Reds star explains why his old club don’t need an out-and-out forward this summer
‘He’ll still be playing at 40 at a good level because he’s in such good shape and looks after himself so well. He does everything to be a top professional’: Ex-Liverpool coach insists Mohamed Salah has plenty more miles in the tank
