Mr Afriyie said: “In the interest of football, I concede defeat and I congratulate my brother.”
But after extensive consultations, officials decided to continue with the third and final round of voting.
Kurt Okraku had won all the elections on the day, making inroads with each round of voting.
Despite polling 44 votes in the first round, the Dreams FC owner gained 15 more votes in the second round to get 59 votes.
Mr Afriyie, on the other hand, had three votes more than the 40 he had in the first round.
The winner was required to get 50 per cent plus one vote to meet the mandatory requirement to head the country’s football governing body.