Ten years ago tensions between the two over the issue led to increased troop deployments along their shared border.
Following Tuesday's meeting in Aleppo, Walid al-Muallem, Syria's foreign minister, told a news conference that Damascus regarded the PKK as a "terrorist organisation banned" in his country.
The foreign, defence, interior, economy, oil, electricity, agriculture and health ministers of the two countries attended the talks in the northern Syrian city.
Anita McNaught, Al Jazeera's correspondent in Istanbul, said the move to improve ties had been welcome on a strategic and a human level with both countries home to families with relatives on the other side of the border.
"This isn't just about visas, this is a complete economic co-operation package," she said.
"Turkey is on an avowed path to resolve old historic disputes, to build better networks in the region, to make the Middle East work better."
Andrew Finkel, a journalist and author based in Istanbul, told Al Jazeera the move did not necessarily signal a change in Turkish foreign policy.
"I don't think Turkey has abandoned its Western orientation but it's on a charm offensive, it's trying to be a good neighbour.
"I think it looks at the map and sees that it has all these countries not just to the west but to the east and the south and that it has its own interest to get along better with those countries, to allow the wheels of commerce to turn, to allow people to cross those borders in a neighbourly fashion."
Earlier on Tuesday, al-Muallem had said: "One week ago, Syria and Turkey carried out manoeuvres near Ankara ... this is important because it refutes reports of poor relations between the military and political institutes in Turkey over its strategic relations with Syria."
Military relations between the two countries developed for the first time earlier this year, causing Israeli media to question arms sales to Turkey, a Nato member.
"The relations between Israel and Turkey are strategic, stretching back dozens of years"
Israel's defence minister
As Turkish-Syrian relations have improved, Turkish-Israeli ties have deteriorated sharply over the past year.
There has been increasing tension between the two countries after Ankara criticised Israel for its December-January assault on the Gaza Strip, which killed more than 1,400 Palestinians.
On January 29, Recep Tayyip Erdogan, Turkey's prime minister, stormed out of a debate on the Gaza war in Davos, Switzerland, after accusing Israel of barbarian acts.
Erdogan told Shimon Peres, the Israeli president, who was sitting next to him at the summit, that "you know well how to kill people".
In the latest sign of worsening ties between the two countries, Ankara called on Israel to show restraint in its reaction to the scrapping last week of an annual air exercise in Turkey in which Israel was supposed to take part.
The Turkish military said last week that the international deployment at the Anatolian Eagle exercise, carried out annually since 2001, had been postponed.
But the Israeli military said the exercises were scrapped because Turkey had excluded Israel, a decision which Haaretz, an Israeli newspaper, said prompted the US to pull out from the drills.
The Turkish foreign ministry said it was "not right to make political conclusions out of the postponement of the exercises".
In a statement, the ministry said: "Assessments and comments attributed to Israeli officials in the press are unacceptable.
"We invite Israeli officials to [use] common sense in their statements and attitudes."
Israeli media have quoted anonymous officials as saying that the sale of advanced arms to Turkey would now be reviewed.
However, Ehud Barak, Israel's defence minister, has cautioned against blowing the incident out of proportion.
"The relations between Israel and Turkey are strategic, stretching back dozens of years," Barak said, according to a statement from his office.
"Despite all the ups and downs, Turkey continues to be a central actor in our region. There is no need to be drawn into hostile statements about them."
The Gaza offensive also led to the disruption of indirect peace talks between Israel and Syria that Turkey had mediated since May 2008.
Davutoglu signalled on Sunday that the Gaza offensive - which killed hundreds of civilians besides Hamas members - and ongoing turmoil in the Palestinian enclave contributed to Turkey's decision to exclude Israel from the drills.
"In the existing situation, of course, we are criticising this approach, the Israeli approach," he told CNN on Monday.
In September, Davutoglu reportedly cancelled plans to visit Israel after he was denied permission to visit Gaza.
Turkey has been Israel's chief regional ally since the two signed a military co-operation deal in 1996.
However, Ankara also has close ties with the Palestinians and supports their struggle for statehood.