The German club have endured a woeful start to the new campaign, recording just five points in eight matches so far as the second-lowest side in the Bundesliga.
And now, Bayer have acted by firing Seoane and replacing him with Alonso following their disappointing 2-0 defeat by Porto in the Champions League on Tuesday.
A club statement confirmed the news on Wednesday. It read: "Bayer 04 Leverkusen have parted company with head coach Gerardo Seoane. The Swiss coach is followed by Xabi Alonso who has a contract to 30 June 2024."
The club's sporting director Simon Rolfes further elaborated on the reasons for relieving Seoane of his duties.
"Gerardo Seoane has done good work for Bayer 04 over the past one and a half years, above all with the outstanding qualification for the Champions League,' he said.
"Unfortunately, we have left the path of success. The early exit from the DFB Cup but in particular the current position in the Bundesliga, which does not meet our expectations, has compelled us to change coaches."
Xabi left his position as Real Sociedad B coach at the end of last season.