The hosts were stunned by Les Aiglonnes at the Accra Sports Stadium as Bassira Toure scored twice to earn her side a 2-1 triumph.
Much of the post-match talks focused on the knight of the whistle, who many local fans claimed was in favoured of the Malians.
“It wasn’t an easy match at all but I will say that about 80 per cent was played by the referee,” Hayford said at the post-match conference.
“I don’t normally talk about referees but referees do frustrate players. And I think the referee succeeded in frustrating our players.
“All the same, I don’t want to take anything away from the Malians but I think on the field of play, we played about 65 to 70% and the referee added whatever she wanted to add.
“I don’t want to complain too much but that is my side of the story.”
Mali’s second goal came from a goalkeeping error when Patricia Mantey failed to claim a free-kick at once, allowing Toure to pounce for the winner. The result gave Les Aiglonnes a first Awcon victory over the Black Queens, who had won all three previous meetings.
“As coaches, we normally don’t put the blame at the doorsteps of one player,” said, Hayford.
“We lost and we have another match to play, for which they need to concentrate and prepare well for. Mistakes are in football. Yes, she made a very terrible mistake and they punished us. We’re going to watch the match again.”
The coach also shed light on his decision to relegate captain Elizabeth Addo and striker Samira Suleman from his starting XI, instead going for 17-year-old Grace Asantewaa and Jane Ayieyam, 21.
“[The decision was] because of their previous performance [against Algeria] and what we saw at the training.
“We wanted to start them from the bench for those who normally come is as substitutes to start today. And they [Asantewaa and Ayieyam] did very well.”
Mali coach Saloum Houssein was simply full of praise for his side.
“We played a difficult game but I will want to take this opportunity congratulate my girls. They played to instructions,” Les Aiglonnes boss said.
“They also played above themselves because when we played against Cameroon, we realized we made a lot of mistakes and were not able to get even a point. It was a very difficult game for us.
“But we decided that for us to remain in this competition, we need nothing but total victory today to stay in the competition and that’s exactly what my girls did.”
Ghana face Cameroon in their last group game on Friday, same day Mali take on Algeria.