The Monaco midfielder headed the winner from a corner as an experimental French team beat an Ivory Coast side filled with familiar names.
"We are a little happy to score in stoppage time but it is part of the game and the match allowed us to involve a lot of players," said France coach Didier Deschamps.
Arsenal striker Nicolas Pepe gave Ivory Coast a 19th minute lead when he drilled a shot off the inside of the near post and past Tottenham goalkeeper Hugo Lloris.
Olivier Giroud replied with a header five minutes later to close in on France's all-time international scoring record.
"He still has this ability to score, especially with his head," said Deschamps.
The former Arsenal and Chelsea moved to 47 goals for France. Thierry Henry leads the list with 51.
"Obviously he was happy about that. He is back in the squad, which he understands well. And so much the better for us," said Deschamps.
The 35-year-old AC Milan striker was recalled when Karim Benzema dropped out injured. Giroud's last France appearance was off the bench as France were eliminated from Euro 2020 by Switzerland last June.
With defending champions France already qualified for the World Cup, Deschamps gave debuts to Christopher Nkunku, who started, William Saliba, who came off the bench after an hour, and 29-year-old Jonathan Clauss, who came on for the last couple of minutes.
"When we have friendly matches, we must take advantage of them," said Deschamps adding that for a second friendly, against South Africa on Tuesday.
"I will make changes to distribute playing time to the maximum number of players."
Saliba, like Matteo Guendouzi, who came on with 15 minutes left, plays for Marseille and were warmly welcomed by the crowd of 62,500 in the Velodrome.
Former Paris Saint-Germain player Adrien Rabiot, on the other hand, was booed when he came on at the end.
Deep into stoppage time, Guendouzi took the corner from which Tchouameni headed the winner.