The case comes as an increasing number of users switches to cheaper Internet-based voice and video services, grabbing market share from telecoms operators.
The Luxembourg-based General Court said Cisco failed to show that the takeover would harm competition.
"Microsoft's acquisition of Skype is compatible with the internal market. The merger does not restrict competition either on the consumer video communications market or on the business video communications market," the judges said.
Cisco, which filed its challenge together with Italian fixed-line and Internet telephone provider and Skype rival Messagenet SpA, can appeal to the EU Court of Justice.
The case is T-79/12 Cisco Systems and Messagenet SpA v Commission.
© Thomson Reuters 2013
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