Barak laid a wreath at the grave of Mustafa Kemal Ataturk, founder of the secular modern Turkish state, praising him as a hero, Ynetnews.com reported.
"We stand here at the grave site with great respect and admiration for the Turkish hero, whose legacy is peace and security," Barack said. "We are inspired by him to try to make our region an area of peace and security."
The visit came amid heavy security and despite calls by Islamic human rights groups for Turkish prosecutors to issue an arrest warrant charging Barak with war crimes in connection with Israel's 2008-09 Operation Cast Lead incursion into Gaza.
It also came during a diplomatic crisis between in the two nations in which Turks say Deputy Israeli Foreign Minister Danny Ayalon insulted Ankara's envoy to Jerusalem last week.
Protesters in the capital Friday had denounced Barak's visit, but none were seen Sunday, Ynetnews.com said. It reported Barak met with Turkish Foreign Minister Ahmet Davutoglu to discuss the diplomatic crisis and was scheduled to meet with Defense Minister Vecdi Gonul.