The 41-year-old will join head coach Sami Hyypiä in the dugout for one last time at Hamburger SV on Saturday, before undertaking his new role as youth team coach.
"I'm happy to have helped over the last 14 months after coming in alongside Sami Hyypiä at a difficult time," said Lewandowski. "Now we've got a team that functions well, has great development potential and plays good, effective football. It wasn't an easy decision to make because it means leaving behind all the work we've put in as a team and the challenge of playing in the [UEFA] Champions League, but at the same time I'm looking forward to the new job."
Lewandowski's coaching career began in the youth ranks at Eintracht Dortmund and SD Wattenscheid 09, before a four-year stint at VfL Bochum (U-17s, U-19s and reserves) took him to Leverkusen's U-19s and senior team in 2007 and 2012 repectively. His new deal runs until June 30, 2016.