In the southern city of Kandahar, the cradle of the Taliban, hundreds of Afghans holding copies of the Quran over their heads marched in protest of the burning.
Demonstrators set cars and businesses on fire in Kandahar. At least nine protestors were killed in and more than 80 injured.
Friday, an angry mob in Mazar-i-Sharif stormed the United Nations compound. They shot four guards and killed three U.N. staff members, beheading at least one of them. In total, 11 people were killed.
The protests come at a critical juncture as the U.S.-led coalition gears up for an insurgent spring offensive and a summer withdrawal of some troops, and with Afghanistan's president increasingly questioning international motives and NATO's military strategy.
Two suicide attackers disguised as women blew themselves up and a third was gunned down Saturday when they tried to enter a NATO base on the outskirts of Kabul, NATO and Afghan police said.
Earlier in the week, six U.S. soldiers died during an operation against insurgents in eastern Afghanistan near Pakistan, where the Taliban retain safe havens.
The Quran was burned nearly two weeks ago but many Afghans only found out about it after President Hamid Karzai condemned it four days after it happened.
The pastor, the Rev. Terry Jones, had threatened to destroy a copy of Islam's holy book last year but initially backed down. On Friday he said Islam and its followers were responsible for the killings.
The Associated Press contributed to this story