Dr Khan was hailed as a national hero for transforming his country into the world's first Islamic nuclear power.
But he was also notorious for having smuggled nuclear secrets to states including North Korea and Iran.
Prime Minister Imran Khan said Pakistan had lost a "national icon".
"He was loved by our nation bec[ause] of his critical contribution in making us a nuclear weapon state," the prime minister tweeted.
Known as AQ Khan, the scientist was instrumental in setting up Pakistan's first nuclear enrichment plant at Kahuta near Islamabad. By 1998, the country had conducted its first nuclear tests.
Renowned nuclear scientist and national icon Dr Abdul Qadeer Khan was laid to rest in Islamabad on Sunday.
His funeral prayers, led by Prof Dr Ahmed Al Ghazali, were held at the Faisal Mosque at 3:30pm.
A large number of people were in attendance during the funeral prayers, despite rain which began to pour shortly after 3pm.
Among those who attended the funeral were cabinet members, parliamentarians and the military leadership.
Two separate enclosures were arranged within the mosque premises, of which one expressly catered to the general public.
'Mohsin-e-Pakistan'
Rasheed showered praise on the scientist, adding that all necessary arrangements were made to save Dr Qadeer's life.
He confirmed that the government will accord a state funeral to the scientist in recognition of his services for Pakistan.
The interior minister said Dr Abdul Qadeer Khan had helped him a lot with educational activities, adding that he had remained a visionary leader in times when Pakistan was going through a sensitive period.
"He is indeed the Mohsin-e-Pakistan," said Rasheed.
The minister later spoke at a press briefing, saying that Prime Minister Imran Khan had directed all cabinet members to attend Dr Abdul Qadeer Khan's funeral.
In response to a question, he said the funeral will be offered at the Shah Faisal Mosque, adding that the public will be allowed to attend it.
"He was a great scientist. He served his country and served it with dignity and hard work," the minister stressed. "The entire country respects him and he will be buried with honour today at 3:30pm."
He informed media that the security has been alerted for the funeral.
Dr AQ Khan is considered the father of Pakistan's nuclear programme and is revered at home as a hero for building the Muslim world's first atomic bomb.
Dr Abdul Qadeer Khan became a national hero overnight, not only in Pakistan but in the Islamic world as well, when in May 1998 Pakistan gave a befitting response to India by conducting its nuclear tests.
Following the tests, Pakistan became the sole nuclear power in the Muslim world and the seventh country to possess nuclear weapons. Pakistan's nuclear weapons have kept Indian aggression in check.
Reactions pour in over Dr Abdul Qadeer Khan's demise
Prime Minister Imran Khan praised Dr Abdul Qadeer Khan by saying that he was, for the people of Pakistan, "a national icon".
"Deeply saddened by the passing of Dr A Q Khan. He was loved by our nation because of his critical contribution in making us a nuclear weapon state. This has provided us security against an aggressive much larger nuclear neighbour. For the people of Pakistan he was a national icon," he tweeted.
President Arif Ali also expressed sadness at his death.
"Deeply saddened to learn about the passing of Dr Abdul Qadeer Khan. Had known him personally since 1982. He helped us develop nation-saving nuclear deterrence, and a grateful nation will never forget his services in this regard. May Allah Bless him," he wrote.
Foreign Minister Shah Mahmood Qureshi expressed his deep sorrow over the demise of Dr Khan. Paying rich tribute to his services for the country, FM Qureshi said that he played a pivotal role in making Pakistan’s defence impregnable.
Besides his research work, Dr Khan used to take an interest in welfare activities, he added. He proved that despite difficult circumstances, one can reach the destination one sets out for oneself, said FM Qureshi.
The foreign minister said that Dr Khan set up a team of scientists and an institution for the country.
Rasheed took to Twitter to post an old picture taken with the nuclear scientist, praying for his forgiveness.
"May Allah provide patience to Dr Abdul Qadeer Khan's relatives and those who are mourning his passing," he added.
Leader of the Opposition in the National Assembly Shahbaz Sharif praised Dr AQ Khan, saying that the country has lost a true benefactor today.
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