Roma were said to be interested in Gian Piero Gasperini, but Atalanta have announced he will lead them in the Champions League next season.
Inter followed Atalanta into the Champions League but their 2-1 win at San Siro on Sunday relegated Empoli.
Atalanta have thrilled in Serie A this season, but Gian Piero Gasperini is desperate to ensure they do not fall short of the top four.
Atalanta denied Massimiliano Allegri victory in his last home game in charge of Juventus, holding the Serie A champions to a 1-1 draw.
Atalanta head coach Gian Piero Gasperini blasted officials after a Coppa Italia final defeat to Lazio.
Lazio were second best for much of the Coppa Italia final in Rome but a pair of late goals downed Atalanta 2-0 on Wednesday.
Marco Baroni's side are the second team to be relegated from Serie A, with Frosinone joining Chievo in dropping down to the second tier.
With four games of the Serie A season remaining, Atalanta are in pole position to take the fourth Champions League place.
Atalanta booked their place in the Coppa Italia final on Thursday and Gian Piero Gasperini wants his players to seize their opportunity.
Atalanta will face Lazio in the Coppa Italia final after beating Fiorentina 2-1 on the day and 5-4 on aggregate.