Moving to quell the furor over an anti-Islam film, he evoked the memory of another leader, assassinated while negotiating with the Taliban.
Karzai also talked to President Obama and expressed condolences over the killing of the U.S. ambassador.
Karzai was to have traveled to Oslo late Wednesday to sign an agreement of strategic partnership.
U.S. is concern that Afghan authorities may simply let some detainees go.
Karzai has called the transfer a victory for Afghan sovereignty.
The handover ceremony took place at the prison next to a sprawling U.S. airfield in Bagram, even as disagreements between the two countries over the thousands of Taliban and terror suspects held there marred the transfer.
It comes as he prepares to name new defense and interior ministers.