The Black Stars conceded just a goal in the qualifiers, ironically against the Harambee Stars in Nairobi last September.
Ghana paid back after Caleb Ekuban's only goal on Saturday became the only ball to end up in the East African's net.
Kenya could have conceded more had Sierra Leone not been disqualified from the qualifiers following their match day 1 defeat to the Leone Stars in Freetown.
Meanwhile, Mali and Senegal were the other teams with the meanest defence after conceeding only two goals in the qualifiers.
Morocco follows with only three goals conceeded.
Twenty four teams have booked their places for the Africa Cup of Nations in Egypt this June with Madagascar, Burundi and Mauritania qualifying for the first time.
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