The Nigerian clean sheet stretched to 494 minutes before Stephen Sarfo broke the deadlock a minute before half-time in a match watched by Confederation of African Football president Ahmad.
Nigeria's consolation goal was scored by Rabiu Ali in the dying seconds of the added time from a free kick given few metres outside the 22metres box of the Black Stars.
Okwudili Nwaolisa, a former Team Manager of Coal-City United FC of Enugu, said since the team had limited time to prepare for the CHAN tournament in 2018 it was necessary for the NFF to retain the players to ensure more blending.
"The group has done well and we now have an idea of our CHAN team", he said.
"Indeed, the match was a true representation of our league".
On Sunday night, hosts and defending champions Ghana thumped long-standing rivals Nigeria 4-1 to retain the sub-regional tournament they also won two years ago. Nigeria goalkeeper Ikechukwu Ezenwa was beaten twice from the spot.
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"We started slowly but we gathered momentum and everything went well for us".
Victory swelled the Ghana Football Association bank balance by US$100,000 thanks to sponsorship from an American news channel, with Nigeria receiving US$50,000.
"For me the level of the competition was high. I'm not happy we lost but all the same I'm impressed by the performance of my players in this competition".
"To be fair to the team, they went for an worldwide tournament without camping, played six matches, five of which they did not concede a goal until the final match".
Balogun will be on parade for the Super Eagles when the face the Chipolopolo's of Zambia in an all important World cup qualifiers in Uyo.