At the annual general meeting in Frankfurt, only 64.7 percent of shareholders voted in favour of it, short of the 75 percent required to adopt the move, the bank said.
The bank had wanted to be able to pay out top performance-based bonuses to some bankers that would have been worth 200 percent of the basic wage.
Such bonuses drew heavy fire as symbols of excess at the height of the world financial crisis, and as instruments that rewarded risky behaviour.
Commerzbank, saved from bankruptcy by the government in 2008, at the request of Berlin capped its top salary at €500,000 ($561,000) per year between 2008 and 2012.
The head of Commerzbank remains fairly modestly paid compared to his peers. Martin Blessing earned €1.4 million last year, according to the company's annual report released this week, and did not get a bonus.