Hyypia, 37, joined Bayer in 2009 after 10 years with Premier League club Liverpool and his contract was due to expire in 2012.
However he has decided to return to Finland to prepare his coaching diploma and will then join the coaching setup at the Finnish national side before returning to Leverkusen in 2012 after the German club offered him a two-year contract as deputy coach.
"My time at Leverkusen has been fascinating and will finish with a direct qualification for the Champions League," said Hyypia, who played 52 times for the club.
"I've spent two years with a superb team and a wonderful club which is giving me the opportunity to start my coaching career."
Hyypia has 105 caps for Finland and won the Champions League with Liverpool in 2005.