The Super Eagles confirmed that Norwich's Yobo, 33, picked up an unspecified strain in the build-up to the midweek friendly and that the 25-year-old Bundesliga defender had been drafted in as his replacement.
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Balogun is the fourth uncapped player named in the Nigeria squad - Ramon Azeez, Imoh Ezekiel and Michael Uchebo were handed a place in preparation for the World Cup in Brazil.
"Balogun has joined the team here in Atlanta," Nigeria's set-up told BBC. "He's very positive and mixing with others players already.
"The game against Mexico is crucial for players like Balogun and others who are keen to make a good impression ahead of the World Cup."
Balogun is eligible to play for either the Super Eagles or Germany due to having a dual nationality, but looks set to favour the African Cup of Nations holders.