Flekken, who has signed a three-year deal with Leverkusen, had been at Brentford since joining from Freiburg in May 2023.
The 31-year-old made 77 appearances for the west London club and helped them finish 10th in the Premier League last season.
“Mark has proven to be a seamless replacement for David Raya, who set an extremely high standard during his years with us,” added Giles.
“We were expecting Mark to be our goalkeeper for many more years, however when Bayer Leverkusen made it known that they wanted to do this transfer, and Mark made it clear that he was interested in moving closer to home and with a possibility of Champions League football, we turned our attention towards how all parties could make this happen.
“Mark has done a great job for us and leaves with our thanks and support.”
Leverkusen recently appointed former Ajax and Manchester United boss Erik ten Hag as their new manager following the departure of Xabi Alonso to Real Madrid.
“Mark Flekken possesses a wide range of skills that a goalkeeper in modern top-flight football must possess,” said Leverkusen sporting director Simon Rolfes.
“Mark exudes an impressive physical presence; from a footballing perspective, he has certainly been one of the best goalkeepers in the Premier League over the past two years.”
