Former Afghan president Hamid Karzai was also among the mourners.
He further said that by creating peace between the two countries, "we can truly recognise the service of Vajpayee".
Atal Bihari Vajpayee death condolences LIVE updates: BJP leader and former Prime Minister passed away at 93 on Thursday, August 16.
Vajpayee, a poet and spellbinding orator respected across the political divide in India, died Thursday after a long period of declining health.
Former Jammu and Kashmir Chief Minister and PDP leader Mehbooba Mufti, Bihar Chief Minister Nitish Kumar, Congress leaders Ghulam Nabi Azad, Mallikarjun Kharge and Anand Sharma, Lok Sabha Deputy Speker M. Thambidurai, former Union Minister A. Raja, MDMK chief Vaiko and TMC leader Dinesh Trivedi were among who witnessed the performance of the last rites. Khan said in a statement that Vajpayee was a prominent political personality of the sub-continent and his death has created a big void.
"Efforts of Mr Vajpayee for improvement in relations between Pakistan and India will be remembered forever", said the cricketer-turned-politician. The Chief Advisor of the Interim Government, Chairman of the Privy Council, and senior government officials also attended the prayer ceremony.
The Dalai Lama, the Tibetan spiritual leader, sent a condolence message to Vajpayee's foster daughter, Namita Bhattacharya, saying India had lost an eminent national leader who had eloquently supported the Tibetan people.
Despite not making a public appearance in years, Vajpayee continued to inspire devotion in many parts of the country, especially in key bellwether Hindu-heartland states in north and central India.
In 2003, the Vajpayee government hosted then Israeli prime minister Ariel Sharon, the first visit by an Israeli prime minister to India.
Caretaker Information Minister Syed Ali Zafar attended the funeral of former Indian premier Atal Bihari Vajpayee on Friday.
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Here's a look at the odds to win this year's event. "If you play well", Peter Uihlein said, "you jump up quite a bit". Jolly finished tied for second in Monday qualifying and earned himself a spot in this week's tournament.