Oracle said it expects to close the transaction shortly and has scheduled a conference call for next week on its strategy for Sun.
The EC had been concerned over MySQL, which Sun bought in 2008. The open-source data-base is seen by some to be in direct competition with Oracle's own database products.
I am now satisfied that competition and innovation will be preserved on all the markets concerned, said Neelie Kroes, the European antitrust commissioner.
Oracle's acquisition of Sun has the potential to revitalize important assets and create new and innovative products.
The European Commission had started an in-depth investigation of the deal in September.
The world's largest business software maker promised in December to keep the market open for others to make enhancements and software for MySQL and said it would be more open than MySQL's previous owners.
It also pledged to invest more in MySQL research and development over the next three years and set up a separate customer advisory board of MySQL users.
The Commission said its decision took into account Oracle's pledges, noting that the company has already begun to implement some of its promises.
The company already received approval from the US Department of Justice last August , while authorities in China and Russia have yet to approve the deal.