Protestors burnt Danish and American flags and an effigy of the Danish prime minister in Karachi.
"They asked us to ban it immediately ... and the order says the ban will continue until further notice," said Wahaj-us-Siraj, convener of the Association of Pakistan Internet Service Providers.
"Users are screaming at ISPs which cannot do anything. The government has a valid reason, but they have to find a better way of doing it. If we continue blocking popular sites, people will stop using the internet."
A knock-on effect from the ban caused some worldwide problems for YouTube. Google, the site's owner, said that the site was unavailable for two hours in some countries.
"Traffic to YouTube was routed according to erroneous internet protocols, and many users around the world could not access our site," Google said in a statement.
"We have determined that the source of these events was a network in Pakistan. We are investigating and working with others in the internet community to prevent this happening again."
The cartoons were first published in 2006 and caused riots in Muslim countries worldwide. Over 100 people were killed and the Danish embassies in Syria, Lebanon and Iran were burnt out.
The images were republished by media outlets the day after police foiled a plot to kill the cartoonist as a statement on freedom of expression.
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