Juventus star Matuidi was diagnosed with a rib problem during medical tests in Turin on Monday, having played 70 minutes of Monday's (AEDT) 1-0 Serie A win over AC Milan.
"The midfielder today underwent an MRI scan, which showed a fracture of the cartilage of the 10th rib," Juve said in a statement.
"I'm unfortunately out of the squad," Matuidi wrote earlier on Twitter.
"But I'm certain that France will get qualification. I'm looking forward to coming back for the next dates."
The French Football Federation confirmed Guendouzi will link up with the squad at Clairefontaine later on Monday.
The reigning world champions will qualify for Euro 2020 from Group H if they beat Moldova in Paris on Thursday, or if Iceland fail to win against Turkey.
"Qualifying has never historically been simple for Les Bleus," head coach Didier Deschamps told reporters on Monday.
"We only took one point from six against Turkey, but the main objective is to qualify.
"It's our goal to finish first, but that's not in our hands anymore because of Turkey. But even if we're first, we wouldn't necessarily be seeded for the draw [for the finals]."
France finish their qualifying campaign with an away game against Albania on November 17.