The EC's decision stated: "The parties' activities mainly overlap for video communications, where Microsoft is active through its Windows Live Messenger.
"However, the Commission considers that there are no competition concerns in this growing market where numerous players, including Google, are present."
The EC's move follows approval by US regulators for the deal in June.
National regulators in Russia, Ukraine, Serbia and Taiwan have yet to rule on the deal.
When he agreed the deal in May, Microsoft chief executive Steve Ballmer said: "Skype is a phenomenal service that is loved by millions of people around the world.
"Together, we will create the future of real-time communications, so people can easily stay connected to family, friends, clients and colleagues anywhere in the world."
The following month Skype dismissed chief marketing officer Doug Bewsher and seven other executives.
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