The two countries signed the protocols under the watchful eyes of big powers
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 establish 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, also including international experts, to examine the "historical dimension" of the two countries' relations.
Kim Ghattas, BBC News, Zurich
And Ankara's role as a broker and stabilising influence would be boosted in a volatile region.
The US also stands to gain. Ties with Turkey, a key American ally, have come under strain repeatedly because of the million and a half Armenian Americans who have lobbied for a draft resolution in the US Congress to name the World War I killings as genocide.
Turkish Foreign Minister Ahmet Davutoglu and his Armenian counterpart, Edward Nalbandian, signed the protocols in Switzerland after a delay of more than three hours.
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 administration of President Barack Obama 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.
Mrs Clinton later said the US would build on the "milestone" that had been achieved, but admitted "concerns on both sides" had delayed the signing.
A senior state department official told Associated Press that Mr Obama had called Mrs Clinton "to congratulate her and the team" on their role in the signing.
The accord needs to be ratified by the parliaments of both Armenia and Turkey.
On Friday thousands of people protested against the deal in the Armenian capital, Yerevan.
"The international recognition of the Armenian genocide will be hindered by this signature, or ratification," said Vahan Hovanissyan, a member of parliament for the nationalist Dashnaktsutyun party.
One protester told the BBC he was not opposed to the opening of the border, but was "against the setting up of a commission that will allow Turkey to further postpone declaring the killings as genocide".
Hundreds of thousands of Armenians died in 1915, when they were deported en masse from eastern Anatolia by the Ottoman Empire. They were killed by troops or died from starvation and disease.
Armenians have campaigned for the killings to be recognised internationally as genocide - and more than 20 countries have done so.
Turkey admits that many Armenians were killed but says the deaths were part of the widespread fighting that took place in World War I.
A roadmap for normalising relations between Turkey and Armenia was agreed in April.
Turkey closed its border with Armenia in 1993 because of its war with Azerbaijan over the disputed region of Nagorno Karabakh.
Correspondents say most people in Armenia feel their landlocked country has been too isolated since the Turkish border closed and are ready for it to reopen.