The 22-year-old will miss the rest of the season after being punished for a breach of contract.
Turkish club Trabzonspor successfully claimed he had agreed to join them in 2013, before staying with Karlsruhe.
"Bayer had nothing to do with the incident," said the Turkey international.
"The club have, however, been affected by the resulting punishment in a sporting and economical sense.
"That's why, for me, it makes complete sense that I should not further harm the club and will therefore forgo my salary during the time of my exclusion."
Leverkusen, who are mid-table in the Bundesliga, face Atletico Madrid in the Champions League last 16.
Bayer Leverkusen attacking midfielder Hakan Calhanoglu says he will not collect his salary during his four-month suspension.