He will be remembered for declaring India a nuclear-armed state while struggling to maintain his image as the moderate face of Hindu nationalism.
A three-time premier, a poet and spellbinding orator, Vajpayee's life in politics spanned five decades but he only attained real power towards the twilight of his career.
His ambition to be recognised as a statesman of international stature led him to put his political neck on the line in seeking peace with rival Pakistan.
But he also brought India out of the nuclear closet with successful weapons tests in 1998 that radically upped the ante following tests deemed peaceful in 1974.
Vajpayee had been in retirement since his Hindu nationalist Bharatiya Janata Party (BJP) was defeated in 2004 elections by a resurgent Congress party.
Long of ailing health, he was hospitalised in June and placed on life support in August. He died a few days later.
A high-caste Brahmin, Vajpayee was born on Christmas Day in 1924 in the central state of Madhya Pradesh.
He toyed with communism before opting to support Hindu nationalist group Rashtriya Swayamsevak Sangh, now parent organisation of the BJP.
He was one of thousands of activists jailed after Congress prime minister Indira Gandhi imposed emergency rule in 1975, and became the BJP's founder-president in 1980, three years after his release.
Vajpayee's formidable parliamentary experience earned him respect across India's political spectrum, with even diehard opponents calling him "the right man in the wrong party".
"Vajpayee is not the BJP. He is an aberration," commented Indian columnist Prem Shankar Jha in 2004.
His three terms as prime minister saw the beginnings of major economic progress and the first period of sustained BJP rule in India, but his legacy came to be defined through the prism of relations with arch-rival Pakistan.
In 1999 he embarked on a historic bus ride to meet then-premier Nawaz Sharif in the city of Lahore, the first time an Indian prime minister had visited Pakistan in 10 years.
Initially, the gamble appeared to have paid off, and Vajpayee was hailed as a visionary peacemaker.
Peace to war
But the goodwill was lost within months as Pakistan-backed militants came across the disputed Kashmir border, seizing Indian military posts in the icy heights of the Kargil mountains and leaving Vajpayee looking like a diplomatic naif who had been duped.
However, Indian troops pushed the intruders back after the 10-week Kargil conflict which cost 1,000 lives on both sides.
An election followed and the BJP traded on Vajpayee's new avatar as "Kargil victor" to return to power at the head of another coalition, marking his transition to a leader of national stature.
After his party lost office, Vajpayee said peace with Pakistan would remain a "lifelong wish" for him.
As premier for the third time, Vajpayee was the glue that held the coalition together; his moderate image allowing his more secular-minded allies to view him as the acceptable face of Hindu nationalism.
He made another bid for peace with Pakistan, inviting President Pervez Musharraf for a summit in July 2001. But the talks collapsed and ties plunged to a new low following an attack on the Indian parliament which New Delhi blamed on Pakistan-based militants.
India responded by massing troops on the border and both countries teetered on the edge of war.
Energetic Western diplomacy defused the standoff but India vowed it would not talk to Pakistan until it ended the flow of militants into Indian-administered Kashmir.
But in the final months of his government's mandate, Vajpayee again offered a "hand of friendship" to Pakistan, resulting in a slow-moving "composite peace process" that reduced frictions for a time.
Vajpayee's persistent peace initiatives came despite him declaring India a nuclear-armed state in possession of advanced weapons following the 1998 tests that drew sanctions from the West.
The unprecedented display of military might drastically upped tensions in South Asia and evoked patriotic fervour and a tit-for-tat response from Pakistan.
Sectarian trouble
Despite his image of religious moderation, Vajpayee was accused at times of failing to pen in BJP extremists.
In 2002, sectarian tensions grew in the wake of a drive by Hindu radicals to build a temple at the site of a mosque razed by Hindu zealots in 1992 in the town of Ayodhya.
The BJP had once been a driving force behind the temple movement that led to the mosque's destruction and Vajpayee struggled to balance secular concerns of his coalition partners against hardliners in his own party who accused him of betraying the BJP's ideological roots.
Vajpayee negotiated a compromise on the Ayodhya dispute but his government was plunged into crisis by an attack on a train carrying Hindu activists.
The assault, blamed on Muslims, sparked some of India's worst communal violence since independence in 1947.
Officials say 1,000 people died, while independent estimates put the toll twice as high.
Remarks by Vajpayee that Muslims were incapable of living in peace with other religions were seized on by the media as evidence of him showing his true Hindu nationalist colours.