Ahmet Davutoglu, Turkey's foreign minister, and Edward Nalbandian, his Armenian counterpart signed the Swiss-mediated deal in Zurich on Saturday, after last-minute disagreements delayed the ceremony for three hours.
"It was pulled back from the brink,' a senior US official said.
Hillary Clinton, the US secretary of state, helped smooth over the disagreement that arose after Turkey objected to an Armenian statement.
The accord is the culmination of more than a year of Swiss-mediated talks.
Besides Clinton, Sergei Lavrov, the Russian foreign minister, and Bernard Kouchner, the French foreign minster, were among those present at the ceremony.
The protocols would still need ratification by their respective parliaments after being signed.
That endorsement will have to come as nationalists on both sides protest the accord, particularly an Armenian diaspora which is demanding that Turkey acknowledge the killings of 1.5 million Armenians during World War I as genocide.Turkey has disputed the claims of genocide, with support from the US and UK, saying that the real death toll is lower.
Many Turks see the fighting as a civil war caused by the collapse of the Ottoman Empire during which an unverifiable number of Turks also died - although both sides agree that more Armenians than Turks were killed.
Both governments have majorities in parliament but are expected to hold back on immediately ratifying the protocols due to the opposition.
Source: Al Jazeera (English)