With the loss, the National Elephants now find themselves at the bottom of the group without a point as they look to recover in their remaining qualifiers.
Group D also features co-hosts Kenya and Eritrea. Kenya have already secured their place at the continental showpiece as one of the tournament's co-hosts, meaning Guinea, South Africa and Eritrea are competing for the remaining qualification spot.
Guinea, who last featured at AFCON in the 2023 edition in Ivory Coast, reached the quarter-finals before their campaign came to an end.
Following the defeat to Bafana, Duarte was asked who he believes will join Kenya at the finals, with the Portuguese coach expressing his dissatisfaction with the way the group was drawn.
"It's an open group first of all," Duarte told the media after the game.
"And I don't understand how the draw was made when you look at the draw actually with the team of Kenya, Eritrea and South Africa I don't think it's fair in terms of the draw."
Despite his concerns, Duarte insists Guinea will fight until the end of the qualifying campaign, with both home and away fixtures still to come.
"But we have more games to play and the away game coming and the game at home as well we will do everything to actually get a result. But I feel the way that the draw was made by CAF is not right, it's not fair."
The Guinea coach has now called on his players to put the defeat behind them and focus on collecting maximum points in their remaining matches.
"Our objective is to qualify for the AFCON. There's different options in terms of going through the qualification. And obviously today we lost the game which is already scratched but we are going to put everything on our side to actually win the remaining games. But we want to win the remaining games so we can advance to the qualification of the AFCON."
Guinea will host the Harambee Stars in their next fixture of the qualifiers on Thursday.