Lewandowski assisted former Liverpool defender Sami Hyypia at Leverkusen during the 2012-13 campaign before serving as interim boss in the closing months of the following season.
He most recently managed German second-tier side Union Berlin but left in March after just six months in charge due to acute fatigue symptoms.
"We are deeply upset and unbelievably sad. Our deepest sympathies and our sincerest condolences go out to Sascha Lewandowski's family and relatives," Union president Dirk Zingler told the club's website.
Leverkusen sporting director Rudi Voller added: "We can scarcely believe that Sascha is dead. He was a great man who brought all his strength and passion to his work."
Lewandowski was found dead in his home, although no cause of death has yet been given.