Commission chief Ursula von der Leyen warned that the bloc has a "tool box" of restrictive measures that be applied "immediately" if Ankara doesn't engage in "constructive" dialogue over underwater drilling.
EU leaders have broken weeks of deadlock and agreed to sanctions on Belarus by reassuring Cyprus and Greece of its "non-negotiable solidarity" over Turkey's underwater drilling.
The European Council vowed to take restrictive measures against Ankara by December at the latest if talks fail.
The breakthrough came after a long day of talks in Brussels on Thursday.
Council President Charles Michel confirmed that there would be sanctions against 40 Belarusian individuals — although President Alexander Lukashenko does not currently feature the list.
The EU pledged to "swiftly" impose sanctions against Belarus in August following the presidential elections whose results it rejected but it was stopped from doing so by Cyprus which demanded the bloc take a much stronger stance against Turkey.
Athens and Nicosia have been in a standoff with Ankara over exploratory drilling in the Eastern Mediterranean. The presence of naval ships in the area has escalated tensions in recent weeks.
'No one can drive a wedge between us'
"We reaffirm strongly the solidarity with Greece and with Cyprus and it is very clear that no one can drive a wedge between us," Commission President Ursula von der Leyen told reporters after the first day of the summit.
She said it was "good" that there is now a "reliable dialogue" between Turkey and Greece, but lamented that Ankara had not offered similar gestures to Cyprus.
"We are convinced that differences must be resolved through peaceful dialogue and in accordance with international law. We want a positive and constructive relationship with Turkey and this would also be very much in Ankara's interests but it will only work if the provocations and pressure stop. We therefore expect that Turkey from now on abstains from unilateral actions," she added.
While EU leaders stopped short of slapping sanctions on Turkey, von der Leyen added that in case of renewed actions by Turkey in the Eastern Mediterranean they would use "all its instruments and options available".
"We have a tool box that we can apply immediately but this is not what we want," she went on.
French President Emmanuel Macron said leaders had reiterated "an intangible and non-negotiable solidarity" with Greece and Cyprus and had decided "to give dialogue a chance" with Turkey.
"If this dialogue is not consistent, it is indeed restrictive measures up to and including sanctions that will be planned in December," he added.
France has upped its military patrols in the Meditteranean over the previous week in a show of support to its two fellow member states.
EU is 'ineffective, visionless, shallow structure'
In a televised address to the nation to mark the 60th anniversary of the country's independence, Cypriot President Nicos Anastasiades expressed "gratitude" to the EU for their "staunch support and solidarity in light of Turkey's provocations".
"I expect from @EUCOuncil a more tangible and effective stance to bring about an end to gunboat diplomacy and for the crisis to be followed by dialogue or recourse to the international court on the basis of international law and the law of the sea," he added.
Greek Prime Minister Kyriakos Mitsotakis said meanwhile that "the time has come for Europe to discuss with courage and sincerity what kind of relationship it really wants with Turkey."
"One thing is certain: Turkish provocation, whether expressed through unilateral actions or extreme rhetoric, can no longer be tolerated," he also said.
Earlier in the day, during an address to parliament, Turkish President Recep Tayyip Erdogan said the "developments in the Eastern Mediterranean constitute the most important battle that Turkey has waged at sea within the last few centuries."
He said Ankara is in favour of "a settlement of disputes regarding the sharing of political and economic potential int he Mediterranean on an equitable basis" but that "the attitude" from Greece and Cyprus "has unfortunately been far from this principle."
The EU he branded as an "ineffective, visionless, and shallow structure".
"There is now a single problem that has emerged in our region that has been solved with the initiative and influence of the European Union. On the contrary, every crisis in which the Union has been involved in has grown by gaining new dimensions," he added