The Norwich City defender is injured and has been replaced in the squad by Leon Balogun, who becomes the fourth fresh invitee to the Super Eagles for Wednesday's clash with El Tri
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.