Erdogan said on Twitter that he and Trump had "agreed to increase our co-ordination on many issues, from our trade relations to developments in Syria" during the "productive" phone call.
According to the Anadolu news agency, both leaders agreed to maintain military and diplomatic co-ordination to avoid the US withdrawal from Syria from being exploited and an authority gap in the country.
During a previous call with Erdogan, the US leader had reportedly gone against the advice of his national security staff and decided to withdraw the 2000 troops on a whim.
US Defense Secretary Jim Mattis resigned after the announcement. His public letter was sharply critical of the president's treatment of allies and was seen as a rebuke of the president's foreign policy.
Days later, the main figure leading the war against Islamic State, Brett McGurk, also stepped down, citing "shock" among partners abroad.
Trump made snide remarks about both men on Twitter. He then decided to move up Mattis' departure date from the end of February to January 1, and announced on Twitter that the deputy secretary of defense, Patrick Shanahan, will become the acting head of the Pentagon.
White House chief of staff Mick Mulvaney - who is the acting replacement for John Kelly, another top official who recently said he is stepping down - admitted on Fox News that Trump's plan is not popular at the Department of Defence.
US lawmakers have expressed concerns about the fate of US partners left in Syria, especially Kurdish fighters who battled against Islamic State extremists at the behest of Washington, as well as a potential vacuum after the forces depart.
Turkey has openly expressed an interest in attacking Kurdish forces in Syria, and Erdogan has previously threatened US troops who were on the ground supporting the local fighters.
French President Emmanuel Macron said on Sunday that he "very deeply regrets the decision made on Syria," adding that "an ally should be dependable," in a sharp criticism of Trump.
Allies around the world have been stunned by Mattis' departure, having seen the former general as a reliable supporter of NATO and other long-standing partnerships. His team often reassured the Kurdish fighters in Syria as well.
During Trump's first year in office, forces completed the takeover of IS's de facto capitals in Syria and Iraq, al-Raqqa and Mosul.
Until Trump's announcement this week on Twitter, administration officials were talking about an extended stay in Syria, pointing to a remaining IS pocket with thousands of fighters, and also expressing a desire to counter Iran and restrain Russia.