Sezer received a warm official and popular welcome, the Syrian News Agency, SANA, said.
This is the second time Sezer has visited the Syrian capital. The first was in 2000 when Sezer attended the funeral of Bashar's father, the late President Hafez Assad.
Relations between the two neighbors had been frosty for decades, chilled by rows over territory, shared water resources and Syria's long-time tacit support for Kurdish separatists fighting in southeastern Turkey.
A thaw began in 1998 when Damascus expelled outlawed Kurdish Workers' Party leader Abdullah Ocalan, whose followers had for years used Syria as a base to fight the Turkish government. Previous to that, the two countries came to the brink of war.
Assad paid a landmark visit to Ankara in January 2004 and bilateral ties have witnessed improvement since then.