Guinea bounced back from their 2-1 defeat to South Africa at the weekend to claim their first points in Group D, while Kenya remain without a win after two matches.
Guirassy, who were kept quiet against Bafana Bafana, made the difference in the 32nd minute. The Borussia Dortmund striker finished to put Guinea in front and give the hosts control of the match.
McCarthy turned to his substitutes after the break, bringing on Timothy Ouma and Ryan Ogam in an attempt to change the game.
Ogam had scored Kenya's late equaliser in their 1-1 draw with Eritrea and almost produced another important moment when he went close 10 minutes into the second half.
The forward found space inside the area, but his close-range effort was denied by Guinea goalkeeper Mohamed Camara.
That proved to be Kenya's best opportunity to get back into the match. Guinea defended their lead well during the closing stages to secure a clean sheet and their first qualifying victory.
Kenya, who have already qualified for the 2027 AFCON as co-hosts, now sit bottom of Group D with one point from two matches.
McCarthy's side face a major test next month when they take on South Africa in a double-header.
South Africa lead Group D with six points, while Guinea have three. Eritrea and Kenya have one point each.
Pitso Mosimane has highlighted the attacking quality of Oswin Appollis and Relebohile Mofokeng after the pair played key roles in Bafana Bafana's emphatic 5-0 victory over Eritrea.
Senegal international Krepin Diatta has secured his next move after joining Championship side Watford on a free transfer following his departure from French club AS Monaco.
Carlos Queiroz has left his role as Ghana coach after the Black Stars suffered a 4-2 home defeat to Gambia in CAF Africa Cup of Nations qualifying.
Benni McCarthy believes Kenya can frustrate Guinea if they maintain their discipline and avoid mistakes in Thursday's 2027 Africa Cup of Nations Group D qualifier at Stade du 28 Septembre.
