The so-called Readmission Agreement is viewed as adding momentum to talks between Brussels and Ankara for Turkey's admission to the EU as a full member, Hurriyet Daily News reported.
Talks on membership resumed last month after a three-year hiatus.
The agreement allows the EU to send back Turkish immigrants who illegally entered member countries.
Thousands of Turks have crossed the border into Greece in recent years, and the EU wants Ankara to take them back.
In exchange, the EU will open talks with Turkey about dropping visa requirements for Turks wanting to travel to Europe.
"The gateway to Europe without a visa will now be open," Prime Minister Recep Tayyip Erdogan said at the ceremony.
The importance of the agreement to Turkey was signified by the presence of Erdogan and three members of the Cabinet.
The agreement calls for lifting visa restrictions within 3 1/2 years, but Erdogan said he hopes that happens sooner to enable citizens from the EU countries and Turkey to interact more.