Garcia joins Bayer on a contract to 2029.
Bayer chief Simon Rolfes said: "Aleix Garcia is a player with exceptional strategic skills, his passes are extremely precise and he plays with great vision.
"Aleix has leadership qualities that will be very valuable to us in the coming years. We are delighted to have been able to sign him and he will be an important factor in achieving our ambitious goals."
Garcia, who scored three goals and provided six assists for Girona last season, sees the move to the German champions as "a great thing".
He continued: "Like fans across Europe, I admired Bayer Leverkusen for their outstanding results this season just finished. I'm thrilled that a club like this has done so much to get me.
"Now I absolutely want to meet all the expectations and give my contribution to this team and the club to continue to be successful."