The deal brings together Beam's brands including Jim Beam bourbon with Suntory's Japanese whiskies and its Bowmore Scotch whisky.
"The Commission concluded that the transaction would not raise competition concerns," the EU executive said on Tuesday.
Reuters reported on April 7 that the deal would go ahead.
Suntory
The deal will boost Suntory's share of the U.S. market to 11 percent from less than 1 percent and give it access to a stronger distribution network in key emerging markets like India, Russia and Brazil.
(Reporting by Robin Emmott; editing by Robert-Jan Bartunek)