The 23-year-old, who has started all six La Liga games this season, lined up alongside Sebastian Caceres in the centre of Uruguay's defence in the 1-0 defeat to Iran.
However, he was quickly replaced by Agustin Rogel in the fifth minute after suffering discomfort in his right abductor muscle.
Araujo's injury is another concern for Barcelona, who already saw Jules Kounde and Memphis Depay sustain injuries for France and the Netherlands respectively.
Kounde had to be withdrawn in the 23rd minute of France's 2-0 win over Austria in the UEFA Nations League, while Depay was also forced off in his country's 2-0 victory against Poland.
Frenkie de Jong and Ousmane Dembele also picked up knocks in their international appearances, which will add to Barcelona's injury worries ahead of a busy schedule with nine matches set to be played in October.