Born in Verona, he started studying violin at the age of seven, and frequented the local Music Academy. Later he studied at the Milan Conservatory and Bologna Conservatory.
He taught composition at the Accademia Nazionale di Santa Cecilia in Rome, Milan Conservatory, and several other Academies and summer courses such as Darmstädter Ferienkurse and Accademia Musicale Chigiana in Siena.
His compositions have been conducted by Claudio Abbado, Pierre Boulez, Bruno Maderna, Salvatore Accardo, Alain Meunier and many others.
At least three generations of composers studied with Donatoni. Among his Italian pupils were Matteo D'Amico, Roberto Carnevale, Giulio Castagnoli, Ivan Fedele, Sandro Gorli, Luigi Manfrin, Giorgio Magnanensi, Luca Mosca, Riccardo Piacentini, Fausto Romitelli, Riccardo Nova, Giuseppe Sinopoli, Alessandro Solbiati, Piero Niro, Giovanni Verrando, and among his foreign pupils Gilles Bellemare, Pascal Dusapin, Javier Jacinto, Magnus Lindberg, Pierre Kolp, Javier Torres Maldonado, Katia Tiutiunnik and Juan Trigos.
One of Donatoni's notable students is the Finnish composer Esa-Pekka Salonen. Donatoni dedicated his final work, "Esa (in Cauda V)," to Salonen, after having dictated it to his assistants from his death bed, and including letters from Salonen's first name as part of the musical material. Prior to the work's world premiere with the Los Angeles Philharmonic, Salonen briefly discussed the piece from the stage: while at first he was too sad to conduct it, he ultimately found joy and affirmation in the piece, noting "my old teacher's message to me, something like 'Carry on, son, it will be OK.'
Donatoni died in Milan in 2000, after dictating his last work, "Esa," to his students.