The step was taken after pressure heaped on the country to stop making a distinction between good and bad militants following a deadly Taliban attack on an army-run school in Peshawar that killed 150 people, mostly children.
A government official said that the decision to ban JuD and several other groups was taken by the government several days ago and tasked the interior ministry to decide the modality to implement it.
The ministry followed by including the name of JuD and Falah-i-Insaniat Foundation, the 2 groups led by Saeed, in the list of banned organisation for their involvement in extremism and militancy.
An official told Dawn newspaper that it was the demand of the United States to ban the Haqqani Network and JuD but the Pakistan government was using "delay tactics".
The decision comes days ahead of US President Barack Obama's visit to India to be the chief guest at the Republic Day Parade on January 26.
Other groups added to the notorious list of banned entities are Harkat-ul-Jihad Islami, Harkat-ul-Mujahideen, Ummah Tameer-i-Nau, Haji Khairullah Hajji Sattar Money Exchange, Rahat Limited, Roshan Money Exchange, Al-Akhtar Trust and Al-Rashid Trust.
After the ban, the assets of these groups will be frozen.
Earlier, an official had said that the government would put the names of JuD on the "watch list" before declaring it as banned group.
The UN Security Council designated the JuD a front for the LeT after the Mumbai attack. Since then, the UN and US have sanctioned several JuD leaders.
The Haqqani network, founded by Jalaluddin Haqqani, has been blamed for the Indian embassy bombing in Afghanistan in 2008 that left 58 people dead, a 2011 attack on the US embassy in Kabul, and several big truck bombing attempts in Afghanistan.
US and Afghan officials have repeatedly said Pakistan's spy agency ISI covertly backed the Haqqanis to extend its influence in Afghanistan, a charge Islamabad deny.
The group was designated as a terrorist organisation by the United States in September 2012.
Pakistan likely to ban Jamaat-ud-Dawa, Haqqani network
'Despite befitting replies, Pakistan not mending its ways'
India's relations with the US must not be one-sided
Journalist among 4 injured in anti-Hebdo protest in Pakistan
Pak boat row: Cong speaking Pakistan language, says BJP