It called on Afghan mujahideen to avenge the film by "dealing a heavy blow" to US forces, and called on religious scholars to "fully inform the masses about such barbaric acts of America ... and to prepare them for a lengthy struggle."
They may have received an unexpected boost from President Hamid Karzai, who also issued a statement condemning the film as an "insult to the greatest Prophet of Islam."
In April last year, violent protests erupted in Afghanistan in response to Mr. Jones burning a Quran in Florida. The event passed largely unnoticed for almost two weeks, until Karzai made a statement to condemn it. An angry mob then overran a UN compound in northern Afghanistan; at least 22 died in nationwide protests.
The violence in Libya and burst of anti-US sentiment deepens the Arab Spring dilemma for President Obama.
"I think that American foreign policy is going to become much more reluctant to provide the support that it is in Libya, and in Syria in particular," says Gerges, referring to the US support for Free Syrian Army rebels at the helm of a 19-month rebellion against President Bashar al-Assad.