The 28-year-old Japanese limped badly after the vault, his second rotation, and barely held the landing following his parallel bars routine where he stumbled backwards.
After being tended to by multiple members of the Japanese delegation and limping around in visible pain, Uchimura gripped up for his high bar routine but then walked off the competition floor at Olympic Stadium.
His absence makes Ukraine's Oleg Verniaiev, who lost to Uchimura by just 0.099 of a point at last year's Rio Olympics, one of the favourites in Montreal.
Verniaiev was a bit shaky as he went out of bounds on the floor exercise and even took a big hop on his high bar routine to finish second in his group behind Cuba's 2015 silver medallist Manrique Larduet.
After three subdivisions, Larduet had the all-around lead with 86.699 followed by China's Xiao Ruoten (86.297) and Russia's David Belyavskiy (85.839). Verniaiev (85.431) was fifth overall.
Men's qualification concludes on Tuesday while the all-around final is Thursday.
Women's all-around qualification begins on Tuesday and there is no clear favourite with many of the top talent, including three-times champion Simone Biles, absent and leaving the stage for their younger successors.
(Reporting by Frank Pingue in Toronto; Editing by Greg Stutchbury)
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