With Cyprus, which lies just 100 kilometres from the Syrian coast, on the fringes of a region wracked by conflict, the three countries say cooperation holds the key to regional stability.
While the alliance has emerged around gas reserves in the eastern Mediterranean, water resources and tourism were also high on the agenda of the talks, said Cypriot government spokesman Nikos Christodoulides.
Netanyahu said the three countries were to form a trilateral committee to study plans to build a pipeline between Israel and Cyprus and on to Greece for gas exports to Europe.
"We're living through great turbulence," the Israeli premier said, referring to the multiple conflicts in the Middle East.
Growing cooperation between the three democracies would advance "stability, security and prosperity" for their peoples and the region at large.
Netanyahu said they also discussed cooperation in water management, tourism, the hi-tech sector and firefighting as well as search-and-rescue missions in the eastern Mediterranean.
"Our partnership is not exclusive in design or nature, and we are ready to welcome other like-minded actors to join our efforts to promote coordination and cooperation, as well as regional peace and stability," the three leaders said in a joint statement.
Netanyahu, for his part, said after that meeting: "Our cooperation with Greece and Cyprus stands on its own... It does not depend on our efforts to normalise our relations with Turkey."
Turkey was a key regional ally of Israel until the two countries fell out over the deadly storming by Israeli commandos in 2010 of a Turkish aid ship, the Mavi Marmara, bound for Gaza.
But the two countries have reportedly been making progress in secret talks aimed at a rapprochement.
Israel has called for Turkey to respect Cyprus's right to explore for natural gas and avoid sparking additional tension in the region.
With Israel finding large reserves of gas close to where Cyprus is drilling, the two countries are looking to cooperate on energy issues such as exporting Israeli gas.
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