The two leaders, who spoke for 30 minutes via videoconference, also discussed upcoming an upcoming meeting of foreign ministers of Muslim nations in Istanbul to discuss aid to drought- and famine-hit Somalia.
They also looked ahead to a December international conference in Bonn on Afghanistan's future and talked about their "work together to forge a long-term strategic partnership," the White House said.
Obama and Karzai discussed "progress by coalition and Afghan National Security forces as security responsibility transitions towards a full Afghan lead in 2014," the statement said.
Obama and Karzai also "discussed their shared commitment to Afghan-led reconciliation and support for a strategy of regional engagement" and "agreed to maintain their close consultations going forward."
The conversation came one day after Obama and his national security team received a briefing from US Ambassador to Afghanistan Ryan Crocker and US and NATO force commander General John Allen.
"The newly arrived team of US leaders in Kabul underscored the continuing momentum of the coalition campaign, development of the Afghan National Security Forces, and support to the Afghan government as they transition to the lead in security," the White House said Thursday.