The Group D encounter in Mongomo appeared to be heading for a dour stalemate as the game entered added time at 0-0.
However, Gyan - who recovered from malaria in time to feature - sparked Ghanaian celebrations with a well-taken 92nd-minute finish.
Gourcuff was particularly disappointed as he felt his team put in an improved showing from their opening victory over South Africa, but suggests the defeat does not change how Algeria will approach their final group match with Senegal.
"It's cruel to lose the game at the last minute," he said.
"But it does not fundamentally change the approach to the last match.
"We were more consistent than against South Africa, we were better with our organisation and defensive solidity."
Gourcuff also feels that the quality of the pitch at the Estadio de Mongomo played a part in Algeria's defeat.
"[We were] unable to find rhythm, because of the condition of the pitch," he added.
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