General Joseph Dunford takes over from US Marine General John Allen, whose 19-month tour was arguably one of the most difficult periods in the war, now in its eleventh year.
"Today is not about change, it's about continuity. What has not changed is the will of this coalition," Gen Dunford told a crowd of foreign and Afghan officials at the headquarters of Nato's International Security Assistance Force (Isaf).
Afghan President Hamid Karzai was absent from the ceremony despite receiving an invitation from Isaf. His spokesman declined to comment.
Gen Allen, who directed transfer of most security across the country to the Afghan army and police, delivered an emotional speech stressing the nation's sovereignty, an issue that has been a thorn in Mr Karzai's relationship with Western backers.
He also stressed the role education is playing in changing the tide of public opinion in Afghanistan against Taliban insurgents.
The White House said last month it would nominate Gen Allen as Nato's supreme allied commander in Europe, after the Pentagon cleared him of professional misconduct over emails linked to a scandal that led his predecessor, David Petraeus, to resign as director of the CIA.