ICE, based in Atlanta, Georgia, is best known as a commodities marketplace. It announced its stock-and-cash offer for NYSE-Euronext, valued at $33.12 per share, in December.
The deal will give ICE control of the New York Stock Exchange and London-based Liffe, Europe's second-largest derivatives market.
"The market investigation revealed that they do not exert a greater potential competitive threat on each other compared to other exchanges," the Commission said in a statement detailing its decision. "Any anticompetitive effects can therefore be excluded."
The combined ICE-NYSE Euronext is slated to become the third-largest exchange group globally, behind Hong Kong Exchanges and Clearing and CME Group.
Commission approval had been widely expected: after a joint bid for NYSE-Euronext by ICE and Nasdaq failed last year, ICE had proactively asked the Commission to examine the new bid.
The Commission said it had examined in particular markets for agricultural commodities, as well as U.S. equity index derivatives.
"The Commission's investigation found that the proposed transaction would not raise competition concerns in any of these fields, as NYX and ICE are offering contracts belonging to different product markets so their activities do not overlap," the Commission said in a statement.
The deal was approved by NYSE-Euronext shareholders earlier this month and is expected to close in the second half of 2013.