The 21-year-old holding midfielder was reportedly a transfer target for both Borussia Dortmund and Borussia Moenchengladbach while also having been linked with a possible move to Real Madrid.
"We are very happy that the most sought after player in the Bundesliga decided to join us," said Schalke sports director Horst Heldt in a statement.
"Johannes possesses enormous qualities. His ability at set pieces, his precise passing game and his vision of where his teammates are make him already one of the best pros in the league in the defensive midfield position."
Geis, who is currently competing with the Under-21 national team at the European championship, joined Mainz in 2013.
He has played 75 Bundesliga matches, scoring six goals.
"Schalke fascinated me, the stadium, the fans," Geis said. "Something new is being created at Schalke and I want to play my part."
Schalke, who replaced coach Roberto Di Matteo with Andre Breitenreiter after finishing sixth in the Bundesliga, will play in the Europa League next season.
(Reporting by Karolos Grohmann; editing by Amlan Chakraborty)
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