The Fortuna Dusseldorf defender fractured his foot minutes after coming on for his debut in Nigeria's friendly with Mexico on Thursday
He is expected to be out for up to eight weeks according to the Nigeria medical team. He will have surgery when he returns to Germany this weekend, said the team's media officer Ben Alaiya.
The Fortuna Dusseldorf defender came on as a second half subsitute for Efe Ambrose but had to leave the game minutes later after fracturing his foot.
The right back clattered into an advertising board after a challenge on a Mexican attacker. He hobbled back onto the pitch to continue but was unable to play further after a few minutes and had to be replaced by Azubuike Egwuekwe.
Balogun was a late replacement for captain Joseph Yobo who was recalled to the side for the first time since February 2013.
The 25-year-old was born in Germany to a Nigerian father from Ijebu Ode while his mother is half Italian and half German. He has expressed his intention to fight for a place in the Super Eagles squad to the World Cup in Brazil.
"I pray my injury heals on time so that I can return to playing football for my club and country,” Balogun was quoted by the Nigerian camp.
Balogun was expected to be a back up to Ambrose who has been the longstanding right back in the squad.