Greek Prime Minister Kyriakos Mitsotakis, Israeli Prime Minister Benjamin Netanyahu, and Cypriot President Nikos Anastasiades attended the January 2 ceremony in Athens to seal the accord for the so-called EastMed project.
The deal comes as Russia prepares to start pumping gas this year through two new pipelines to Europe -- TurkStream and Nord Stream 2. Russian President Vladimir Putin and Turkish leader Recep Tayyip Erdogan are scheduled to launch TurkStream on January 8.
The three MedStream governments will next put the project out for bids from private investors for financing.
The countries hope to reach a final investment decision by 2022 and aim to have the pipeline completed by 2025.
European governments and Israel agreed last year to proceed with the project, valued at up to $7 billion.
It is expected initially to carry 10 billion cubic meters of gas annually from Israeli and Cypriot waters to the Greek island of Crete. It would then move on to the Greek mainland and into Europe's gas network through Italy.
Turkey has opposed the EastMed pipeline, saying it would not allow these types of projects without its participation or approval in the eastern Mediterranean.
Ankara also accused the three countries of attempting to encircle Turkey. Greece and Cyprus have a long history of bitterness with Turkey, and Israel has also had difficulties with Ankara.
The United States and the European Union support the project, with Washington often stressing the need for Europe to become less dependent on Russia for natural gas supplies.
Officials have also said they hope the deal could help spur additional investment in the natural gas sector in the Middle East.
The rival TurkStream project will carry a maximum of 31.5 billion cubic meters of Russian gas annually to Turkey. Some of the gas will be exported further to Europe through Greece.
Russia expects to launch Nord Stream 2 to Germany through the Baltic Sea by the end of the year.
The EastMed pipeline would potentially compete for Balkan gas markets with TurkStream.
U.S. Secretary of State Mike Pompeo was scheduled to visit Cyprus on January 7 to discuss EastMed, but his visit was delayed due to attacks on the U.S. Embassy in Baghdad.
The U.S. Congress last month passed a bill that sets aside $1 billion to support energy infrastructure projects in Eastern Europe with the aim of reducing the region's dependence on Russia.