The Ivory Coast international could be out for as long as six weeks with the hamstring injury, according to reports.
Kessie is therefore sidelined for Barca's last two games, against Almeria and Osasuna, before the international break for the FIFA World Cup.
"He is screwed. I think he has hurt his hamstring. He was playing a good game in the midfield position, winning duels, and was good at the start," said Barca boss Xavi Hernandez, as quoted by Barca Universal.
Kessie joins a long list of recent Blaugrana ailments, as Jules Kounde, Ronald Araujo, Memphis Depay, Frenkie de Jong, Andreas Christensen, Hector Bellerin, Sergi Roberto, and Eric Garcia have all picked up knocks of one sort or the other since the last international break.
The 25-year-old is only expected to return to action for the clash with Espanyol in LaLiga at the end of the year.
Barcelona have been eliminated from the Champions League after finishing third, behind Bayern Munich and Inter, in Group C despite beating fourth-placed Plzen.