"Assad and his regime are the source of instability in Syria now and pose the greatest danger to fanning flames of sectarian conflict not only in Syria but beyond," Biden told Abdullah Gul when they met Friday, the senior official told reporters.
Assad is from Syria's Alawi minority, while the anti-regime protesters are overwhelmingly from the Sunni majority.
Alawis loom large in the pro-regime militias who have taken a leading role in the regime's brutal crackdown that has claimed more than 4,000 lives according to UN figures, sparking mounting sectarian violence in protest centres such as third-largest city Homs.
In the region, Assad's main ally is Shiite Iran.
Biden said the "number one objective" was to get the Syrian regime to stop killing civilians and for Assad to quit power, the official said.
Biden, who arrived to Turkey from Iraq, urged Assad to quit power in an interview with the Turkish daily Hurriyet published Friday.
"The United States' position on Syria is clear. The Syrian regime must end its brutality against its own people and President Assad must step down so a peaceful transition that respects the will of the people can take place," Biden said.