The 29-year-old pulled out of a move to Sampdoria in favour of joining Atalanta, who finished an impressive fourth in Serie A last season.
The completion of the attacking midfielder’s switch was announced on Wednesday, with no further details provided, as reports in Italy suggest he has cost around €5.5million.
Ilicic spent four seasons with Fiorentina, racking up 105 Serie A appearances.
His best campaign saw him score 13 times and produce five assists in 2015-16.
Last season he netted five goals and added a further four assists in 29 league outings as the Viola finished eighth.
Ilicic, a Slovenia international, had previously played for Palermo in Serie A.