The watered-down statement, which came after days of arguments among member states, did not follow the lead of the United States in specifically calling on China to honour the decision by the UN-backed tribunal in The Hague.
EU foreign policy chief Federica Mogherini said in a statement that the bloc's member states "acknowledge" the ruling but said the EU does not take a position on sovereignty rows.
"The EU calls upon the parties concerned to address remaining and further related issues through negotiations and other peaceful means and refrain from activities likely to raise tensions," Mogherini said.
The statement came after days of wrangling over wording as eastern EU countries, including Slovenia and Croatia which also have territorial disputes before the tribunal, diplomats said.
"Two member states (Croatia, Slovenia) have a principle problem with arbitration judgements," an EU diplomat told journalists on condition of anonymity.
China asserts sovereignty over almost all of the strategically vital waters, despite rival claims from its Southeast Asian neighbors, most notably the Philippines.
China's claims, which include waters approaching neighboring countries, are based on a vaguely defined "nine-dash-line" found on a 1940s Chinese map.
The row has embroiled the United States, which has deployed aircraft carriers and a host of other vessels to assert freedom of navigation in the waters -- through which a third of the global oil trade passes.
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