Saturday's meeting was their first since Karzai visited Obama at the White House in May.
Karzai told Obama he set the right tone for Saturday's NATO session, which focused on Afghanistan. At the session, NATO countries formally agreed to begin turning over Afghanistan's security to its military next year and to give local forces full control by 2014.
Obama wants to start pulling U.S. forces out of Afghanistan in July.
Karzai recently demanded that NATO reduce its military operations in Afghanistan and stop nighttime raids against suspected Taliban leaders.