Perle composed with a technique of his own devising called "twelve-tone tonality". This technique was different from, but related to, the twelve-tone technique of the Second Viennese School, of which he was an "early admirer" and whose techniques he used aspects of but never fully adopted. Perle's former student Paul Lansky described Perle's twelve-tone tonality thus:
Basically this creates a hierarchy among the notes of the chromatic scale so that they are all referentially related to one or two pitches which then function as a tonic note or chord in tonality. The system similarly creates a hierarchy among intervals and finally, among larger collections of notes, 'chords.' The main debt of this system to the 12-tone system lies in its use of an ordered linear succession in the same way that a 12-tone set does".
In 1968, Perle cofounded the Alban Berg Society with Igor Stravinsky and Hans F. Redlich, who had the idea (according to Perle in his letter to Glen Flax of 4/1/89). Perle's important work on Berg includes documenting that the third act of Lulu, rather than being an unfinished sketch, was actually three-fifths complete and that the Lyric Suite contains a secret program dedicated to Berg's love-affair.