The two discussed the results of the Kurdistan Regional Government (KRG)'s independence referendum - which saw the 'yes' vote win with 92 percent- and regional developments as well as bilateral relations between the two countries, the prime minister's office said in a statement.
The Turkish military and the Iraqi army are currently conducting joint military drills at the border, which have been ongoing since last week.
Iraqi lawmakers earlier passed a resolution calling on Abadi to "take all necessary measures to maintain Iraq's unity" including by deploying security forces to disputed areas.
The resolution also called for the closure of border posts with Turkey and Iran that are outside central government control.
Turkey as well as Egypt, Jordan and Lebanon said Wednesday they will halt flights to and from Iraqi Kurdistan this week until further notice at the request of Baghdad.
More than 92 percent of Iraq's Kurds voted "Yes" for independence in the referendum, according to the first official results announced on Wednesday, two days after the disputed plebiscite.
Abadi had said he would ban "international flights to and from Kurdistan" from Friday unless the airports in Irbil and the city of Sulaymaniyah were placed under the control of the federal government in Baghdad.
Baghdad has consistently said that Monday's referendum constituted a violation of Iraq's constitution.
Monday's controversial referendum had faced wide-spread opposition from most regional and international actors, many of whom had warned the poll would further destabilize the region and distract from the ongoing fight against Daesh.
