Turkish Foreign Minister Ahmet Davutoglu and his Armenian counterpart, Edward Nalbandian, signed the protocols in Switzerland after a delay of more than three hours.Turkey and Armenia have signed a historic accord normalising relations after a century of hostility.
The deal was signed by the two foreign ministers after last-minute problems delayed the ceremony in Switzerland.
Under the agreement, Turkey and Armenia are to resume diplomatic ties and reopen their shared border.
The accord has been met by protests in Armenia, where many people say it does not fully address the 1915 killing of hundreds of thousands of Armenians.
Armenia wants Turkey to recognise the killings as an act of genocide, but successive Turkish governments have refused to do so.
The agreement calls for a joint commission of independent historians to study the genocide issue.
The BBC's Kim Ghattas in Zurich says the Armenians had apparently raised objections to remarks due to be read out by the Turkish delegation.
After the signing neither side issued a statement, and our correspondent says this seems to have been the compromise arranged by US officials.
The Obama administration had been pressing the parties to reach agreement.
The ceremony was attended by US Secretary of State Hillary Clinton, as well as Russian Foreign Minister Sergei Lavrov and the EU's High Representative for the Common Foreign and Security Policy, Javier Solana.
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BBC NEWS | Europe | Armenia and Turkey normalise ties