The 38-year-old astronaut said during the presentation that “the stone was a very important guest on the space station.”
The piece of the cathedral accompanied Gerst on a six-month mission on the International Space Station in 2014, orbiting the earth 2,566 times and travelling a total of 110 million kilometres.
A spokesperson for the mayor's office told The Local that Gerst had taken the stone into space "to have a piece of home with him as he went.” She added that he had also taken a flag with the city's coat of arms on it into space.
The spokesperson reported that students from 15 schools attended the event, at which Gerst gave a presentation on his experiences in space and the research he had done.
Gerst told the students that his view from space had taught him about the fragility of our environment and the need to protect the world's ecology.
The mayor of Cologne, Jürgen Roters, told the assembly that he was grateful to Gerst that he had telephoned him personally while he was in space.
The stone is set to remain on display at the Cologne town hall.
Gerst also commented on Wednesday on the Germanwings plane crash.
“When I learnt about the event it was a shock. It is an unbelievable tragedy," he said. "It is completely sad when so many people lose their lives."