The talks, more symbolic than substantial, went ahead after EU foreign ministers overcame last-minute objections from Cyprus which wants Ankara to open its ports and airports to Cypriot ships and planes.
"We have completed an important milestone in relations between Turkey and the EU," said a smiling Turkish Foreign Minister Abdullah Gul at a late-night press conference with EU leaders in Luxembourg.
"This will be remembered as an important step in the future," he added.
Mr Gul flew in from Ankara for the talks, on the first of 35 policy "chapters" to be negotiated before the vast mostly Muslim country can join the EU.
The negotiating session was largely formal, and the discussions - on the non-contentious issue of science and research - were completed almost straightaway.
EU enlargement commissioner Olli Rehn also hailed the talks, but warned that Ankara needs to do more, and in particular implement the Ankara protocol, if it is to avoid a "train wreck."
"We have to use this current window of opportunity. I truly appeal to all parties to try their best ... to improve the climate and start real work, less focus on past injustices, more focus on future solutions," he said.
"Otherwise we don't get anywhere and … it's very difficult to avoid such a train crash."
Cypriot recognition
Ankara won an EU green light last October to start membership talks, but only after allaying critics who wanted Turkey to be offered a "privileged partnership" rather than full EU membership.
But Cyprus, which as a member state has power of veto, had refused to agree to the first detailed talks until Turkey recognised the Greek Cypriot government and fully implemented the so-called Ankara protocol.
Cyprus has been divided since 1974 when Turkey occupied the northern third in response to an Athens-engineered Greek Cypriot coup seeking to unite the island with Greece.
Monday's talks were on science and research, the first and possibly the least contentious of 35 policy "chapters" to be covered during negotiations with Ankara which are expected to last at least a decade.
The Greek-Cypriot government had pressed for the accord with Turkey to include an explicit demand for Turkey to ratify the Ankara pact, to allow Cypriot ships and planes into Turkey.
But other EU states had argued for simply a reference in the text to an EU declaration made last September which itself set out in details the demands.
Warning to Ankara
In the event, the key paragraph at the centre of the diplomatic dispute steered a fine line between the two versions - and included the clear warning to Ankara.
French minister Philippe Douste-Blazy echoed the warning, saying: "If at any moment the (EU) commission judges that the criteria are not met we should not be afraid to say it."
Turkish Prime Minister Recep Tayyip Erdogan shrugged off the threat, referring dismissively to "a part of Cyprus"
"Currently I do not believe ... members of the European Union would pay a lot of attention to that veto of a part of Cyprus," he said, speaking during a visit to Croatia.
More broadly, Turkey's EU hopes have been seriously clouded by the institutional turmoil into which the European bloc was plunged last year, when French and Dutch voters torpedoed the EU's hard-fought constitution.
But Turkey's historic foe Greece, whose ties with Ankara have warmed in recent years, welcomed the accord to start talks.
"This is a positive development for everyone after some complicated and difficult negotiations," said Greek Foreign Minister Dora Bakoyannis.
The Cypriot minister meanwhile warned that Turkey faces an "absolute deadline" of October - when the EU commission is to report on Turkey's progress - to open its ports and airports to Cypriot ships and planes.
"It has to implement all the undertakings it made" under the protocol," the Cypriot minister said. "If it doesn't it will prejudice the conduct of the negotiations.
"This message has gone out loud and clear today," he said.