The bill, passed by 320 to 129, also permits strikes against Syrian targets.
But Deputy Prime Minister Besir Atalay insisted this was a deterrent and not a mandate for war.
Turkey has been firing at targets inside Syria since Wednesday’s shelling of the town of Akcakale, which killed two women and three children.
Ankara’s military response marks the first time it has fired into Syria during the 18-month-long unrest there.
The Turkish parliament passed the bill in a closed-doors emergency session.
It permits military action, if required by the government, for the period of one year.
However, Besir Atalay insisted the priority was to act in co-ordination with international bodies.
He told Turkish television: “This mandate is not a war mandate but it is in our hands to be used when need be in order to protect Turkey’s own interests.”
He said Syria had accepted responsibility for the deaths.
“The Syrian side has admitted what it did and apologized,” AFP news agency quoted Besir Atalay as saying.
The UN Security Council is to meet later, following a Turkish request for the body to take “necessary action” to stop Syrian “aggression”.
NATO has held an urgent meeting to support Turkey, demanding “the immediate cessation of such aggressive acts against an ally”.
The US, the UK, France and the European Union have already condemned Syria’s actions.
Russia, which is allied to President Bashar al-Assad’s government, has asked Damascus to acknowledge officially that the cross-border attack was “a tragic accident” which will not happen again.
Many social media users in Turkey have been reacting strongly against the possibility of war with Syria.
There were many tweets referring to the call for an anti-war rally in central Istanbul on Thursday evening.
In Syria itself as many as 21 members of Syria’s elite Republican Guards have been killed in an explosion and firefight in the Qudsaya district of Damascus, said the UK-based Syrian Observatory for Human Rights (SOHR).
The SOHR is one of the most prominent organizations documenting and reporting incidents and casualties in the Syrian conflict. The group says its reports are impartial, though its information cannot be independently verified.
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