The imposing centre back, who is regarded among the best in European club football, was cautioned for a second time in three matches after conceding a penalty in Sunday's 1-0 semi-final win over Tunisia in Cairo and will be suspended for the final.
"It's a shame we will be without Kalidou, he's vital in this team, a player who gives us a lot. We will also be playing for him," midfielder Pape Alioune Ndiaye told reporters after the extra-time triumph at the 30 June Stadium.
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Koulibaly, who plays in Serie A for Napoli, was struck on the elbow by a fearsome shot by Ferjani Sassi as he turned his back, attempting to get his body in the way of the shot.
It was utter bad luck for the 28-year-old but there would have been a measure of relief when Sassi then botched the subsequent spot kick.
Minutes later Senegal missed a penalty of their own and the game then went into extra time where a bizarre own goal from Dylan Bronn settled a match distinguished by the high number of foibles.
Senegal coach Aliou Cisse saw it differently after his side booked a place in the final for only the second time.
"The match was incredible, it will remain in the annals of African football," he told the post-match news conference.
"It's the charm of football, this excitement. We cannot control anything at all."
It will be a second final for Cisse, who was captain when Senegal made their only previous appearance in 2002 to lose on penalties.
"There is a pride at getting to the final. It had been 17 years since we got this far, since my generation in 2002," Cisse said.
"Our philosophy is to take a game at a time and try to play the best football to erase the disappointment of 2002. It's a dream to win the title not only for me, but for all the Senegalese people.
"We are close to realising this dream that we could not achieve in 2002."
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