In the sixth stage, Aucouturier, M.Garin and Dortignac escaped in the last kilometres. Aucouturier signed first at the control post in Ville-d'Avray. From that point, the race was neutralised until the velodrome Parc-des-Princes, where the riders would ride the final kilometre. At the moment that the riders arrived in Paris, it started to rain. The organisers decided together with the cyclists to exclude the final kilometre from the race, and make the control post in Ville-d'Avray the end of the race. This made Aucouturier the winner of the stage. Maurice Garin finished second, which made him the overall winner, untill December 1904 that is. At the bottom of this page are the 12 names of riders who were disqualified by the UVF (Union Vélocipédique Française) because of, among other actions, illegal use of cars or trains. The Tour organizers were happy with the original result, but the UVF started an investigation after complaints from other cyclists. Their investigative committee heard testimony from dozens of competitors and witnesses, and, in December 1904, disqualified all the stage winners and the first four finishers (Maurice Garin, Pothier, César Garin, and Aucouturier). Nine of those disqualified were banned for one year, Garin for two years and the remaining two for life. In total, 29 riders were punished. The reasons for the disqualification were never made public.

Fifth-placed Henri Cornet, aged 19, then became the youngest ever winner of the Tour. Cornet had also been warned after he had received a lift by a car. Only 15 cyclists from the original 27 that finished were not disqualified.

Following the disqualifications, the Tour de France came nearest in history to being permanently cancelled. The race organiser Henri Desgrange, said he would never run the race again because it had been overtaken by the "blind emotions" of those who attacked or helped riders as they passed. Desgrange was also upset that the UVF had imposed judgement on his race when he had already disciplined riders as he saw fit.

An angry exchange ensued between Desgrange and the UVF but the letters and the detailed complaints that led to the UVF's actions were lost when the Tour de France archives were transported south in 1940 to avoid a German capture and were never seen again.

Until the end of his life, Garin always said that he was the rightful winner of the 1904 Tour de France, but according to Les Woodland, an English born French cyclist and later cyclist-writer from the Toulouse area, Garin confessed to a friend that he had cheated.