The latter company is a renewable energy business, with RWE as the controlling shareholder currently.
E.ON also intends to swap a number of assets with RWE as it aims to solely focus on providing energy networks and services to retail customers.
RWE will acquire E.ON and innogy’s renewable businesses and take a 16.7% stake in the energy firm.
The Commission will now examine the possible effects of the transaction on competition in Europe.
Johannes Teyssen, CEO of E.ON said: “With the filing of the transaction in Brussels, we have taken an important step towards our goal of implementing the transaction agreed with RWE to acquire innogy from mid-2019.
“With the integration of innogy, we want to further develop the new E.ON into a clearly focused operator of European energy networks and provider of modern customer solutions. And we want to develop innovations even more powerfully than before to improve the lives of our customers and drive the energy revolution in Europe.”