Karzai, who described the images as "inhumane and provocative," said "the only way to put an end to such painful experiences" was to end the presence of foreign forces in Afghanistan.
"It is such a disgusting act to take photos with body parts and then share it with others," he added.
U.S. Defense Secretary Leon Panetta has also condemned the photos, reportedly taken in 2010 and published Wednesday by the Los Angeles Times, saying they depict behavior that "absolutely violates" U.S. regulations and values.
A military investigation is under way.
The row is the latest strain on tense U.S.-Afghan relations following a string of incidents that have plagued the U.S. military in Afghanistan this year.
A massacre of villagers in March, allegedly by a U.S. soldier, led Karzai to demand that foreign troops withdraw from Afghan villages and return to their larger bases.
In a statement Thursday, the Taliban said what the photos show is typical of what the United States stands for.
"In the last 11 years since the Americans invaded Afghanistan, they have repeatedly done inhumane things which are not acceptable to anyone in the world," the Taliban said.
NATO Secretary-General Anders Fogh Rasmussen said Wednesday the images "don't in anyway represent the principles and values that are the basis for our mission in Afghanistan." He added that he considers the photos "an isolated event."
The two photos published by the paper are among 18 provided by a U.S. soldier who wanted "to draw attention to the safety risk of a breakdown in leadership and discipline," the Los Angeles Times reported.
One shows a member of the U.S. military in front of what appears to be the body of an insurgent. The photo shows the insurgent's head, with his eyes open and what may be his hand on the American soldier's shoulder. Another soldier appears to be looking down at the body, reaching his hand into the blanket covering it.
The second photo shows a group of people, including some American soldiers, standing with what appear to be legs from a corpse. One U.S. soldier is smiling and giving a double thumbs-up, and another is also smiling at the camera. There appear to be Afghan police in that photo as well.
CNN has not authenticated the images.
The photos' release is the latest in U.S. military setbacks this year in Afghanistan.
In January, a video posted on a website showed four U.S. Marines urinating on enemy corpses.
A month later, International Security Assistance Force personnel at Bagram Air Base improperly disposed of Islamic religious materials, including Qurans, by burning them in what U.S. officials described as an unintentional error.
In the March attack, Army Staff Sgt. Robert Bales allegedly left a remote outpost in Kandahar province's Panjwai district and went house to house, gunning down villagers. He has been charged with 17 counts of murder in the shooting rampage.
The attack intensified a debate about whether to pull American troops ahead of their planned 2014 withdrawal.