The change will take effect on September 24.
Commerzbank CEO Martin Zielke said it "of course, it is not welcome" that Germany's second-largest lender and a founding member of the prestigious DAX club three decades ago has to move to the mid-size MDAX index.
"But nothing changes for our customers and our business."
The ailing bank, which had to be rescued by the German state during the financial crisis, has seen its share price plunge by a third since January to give it a market cap of just over 10 billion euros ($11.5 billion) - the lowest of all DAX 30 players.
Investor darling Wirecard, currently listed on the TecDAX index, had been widely expected to take Commerzbank's spot in the reshuffle.
The so-called "financial technology" (fintech) company that makes software for cashless and contactless payments has seen its share price soar by 110 percent this year.
It has a market cap of over 23 billion euros, surpassing even flagship lender Deutsche Bank which is valued at some 20.5 billion euros - and was itself axed from the eurozone's benchmark Eurostoxx 50 index on Monday.
Wirecard is now the country's third-largest financial group on the German stock market behind insurance behemoths Allianz and Munich Re.