Lauding his role regarding Pak-India bilateral relations, Imran Khan stated that his contribution will never be forgotten.
The PTI chief stated that there could be political differences between the two countries, however, the desire to establish peace existed on both sides of the border.
Vajpayee, 93, passed away at the All India Institute of Medical Sciences here on Thursday evening after a prolonged illness.
But in India he was hailed as a hero, and it helped him bolster his image as a leader who was serious about national security and not afraid of global pressure. The government conferred the Bharat Ratna, India's highest civilian honour, on him in 2015.
This was a silent gesture of PM Modi to show how much he loved and respected BJP stalwart AB Vajpayee.
He was a lifelong poet who revered nature but who oversaw India's growth into a swaggering regional economic power.
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Khan said that Vajpayee started efforts for improving Indo-Pak ties and continued them after becoming prime minister. "The world will celebrate him as an exemplary statesman", read the message posted on Twitter by Bhutanese prime minister Tshering Tobgay.
Mr Modi said Mr Vajpayee's stewardship put India on a fast track to growth. Israel supplied key munitions and weapons to India in 1999 during the Kargil war as India battled Pakistani insurgents and army regulars.
Many of them would never have visited the BJP headquarters otherwise.
He first became the prime minister of India for only 16 days - May 16-31, 1996 - and was re-elected PM in March 1998, where he remained in office until May 13, 2004.
The flag will fly at half mast and Vajpayee will be accorded a state funeral, the government has also decided. "EAM @SushmaSwaraj met with former President of Afghanistan Hamid Karzai and leaders talked about great role played by former Prime Minister Shri Atal Bihari Vajpayee in consolidating democracy in Afghanistan", the MEA spokesperson tweeted.
"Deepest condolences conveyed by our friends from Nepal on the loss of a visionary leader!"