Uchimura, who won silver in the All-Around four years ago in Beijing, was not at his scintillating best but scored 92.690 to see off the challenge of German Marcel Nguyen in silver medal position with USA athlete Danell Leyva in bronze, just under two points off the lead.
USA athlete Leyva topped qualification ahead of Russian David Belyavskiy and Germany's Fabian Hambuchen with Uchimura down in ninth place.
However, Leyva and Hambuchen both faltered on the Pommel Horse, with the German having an inquiry into his score rejected, leaving the door wide open for their Japanese opponents, Uchimura and Kazuhito Tanaka, as Belyavskiy also looked slightly below par.
Parallel Bars world champion Leyva battled back from his shaky start and put himself in medal contention with a strong set on the Rings, an efficient Vault and excellent Bars routine.
As the American hit back, Nguyen - the reigning European Parallel Bars champion, scored 15.833 on his specialist piece of apparatus before a strong High Bar routine lifted him into the medal positions with one rotation to go.
Japan's Tanaka then saw his medal hopes disappear thanks to a costly fall on his final piece of apparatus, the Pommel Horse, to drop him into sixth place after he had spent the majority of the competition in second.
As Uchimura played it safe on the High Bar then finished off on Floor, smiling to the crowd safe in the knowledge he had secured his first Olympic Games gold medal, Leyva moved up into silver medal position after nailing his High Bar routine.
But Nguyen - the last gymnast to finish - was not done, scoring 15.300 on his final piece of apparatus, the Floor, to snatch silver from the USA athlete in a dramatic finale.