Widor's best-known piece for the organ is the final movement of his Symphony for Organ No. 5, a toccata, which is often played as a recessional at wedding ceremonies and at the close of the Christmas Midnight Mass at Saint Peter's Basilica, Vatican City. Although the Fourth Symphony also opens with a Toccata, it is in a dramatically different (and earlier) style. The Toccata from Symphony No. 5 is the first of the toccatas characteristic of French Romantic organ music, and served as a model for later works by Gigout, Boëllmann, Mulet, Vierne and Dupré. Widor was pleased with the worldwide renown this single piece afforded him, but he was unhappy with how fast many other organists played it. Widor himself always played the Toccata rather deliberately. Many organists play it at a very fast tempo whereas Widor preferred a more controlled articulation to be involved. He recorded the piece, at St. Sulpice in his eighty-ninth year; the tempo used for the Toccata is quite slow. Isidor Philipp transcribed the Toccata for two pianos.

Over his long career, Widor returned again and again to edit his earlier music, even after publication. His biographer, John Near, reports: "Ultimately, it was discovered that over a period of about sixty years, as many as eight different editions were issued for some of the symphonies."