Mrs Patil's backers say her election will be a boost to women
Mrs Patil, 72, won nearly two-thirds of votes cast in state assemblies and in India's parliament, they said.
The former governor of the northern Indian state of Rajasthan described her win as "a victory of the people".
Mrs Patil's supporters say her election to the largely ceremonial role will be a boost to millions of Indian women.
The BBC's Sanjoy Majumder, in Delhi, says that while some see her victory as an important step towards gender equality in India, many view it as only a symbolic gesture.
Millions of women in India face discrimination and poverty often linked to age-old traditions which require the parents of a bride to pay a large dowry to the family of her eventual husband.
Women's landmark
Mrs Patil emerged as a surprise, last-minute candidate after left-wing parties in the Congress-led coalition opposed the Congress Party's first choice.
She was backed by Congress leader Sonia Gandhi, but was mocked by opponents and by some sections of India's media.
This is a victory for the principles which our Indian people uphold
Pratibha Patil
Profile: Pratibha Patil
But Mrs Gandhi, the Congress Party leader, hailed her candidate's win.
"In the 60th year of our independence, for the first time we have a woman president," she said.
"I am grateful to the people of India and the men and women of India and this is a victory for the principles which our Indian people uphold," the Reuters news agency quoted Mrs Patil as saying after her victory was confirmed.
There was also support at a hostel Mrs Patil established in Mumbai, in her home state of Maharashtra.
"It is encouraging for other women who want to step out of their homes and make something out of their careers or do something in the world," said one resident, Priya Mehra.
Balancing role
Mrs Patil has courted controversy, recently telling a Muslim congregation that the veil was introduced to protect their women from Mughal invaders, a comment she later retracted.
She also faced allegations that a bank she helped set up gave out cheap loans to her relatives before it folded up.
The Congress Party has rejected those allegations and was highly critical of the Bharatiya Janata Party (BJP)-led opposition candidate, Vice-President Bhairon Singh Shekhawat, an 83-year-old party veteran.
The presidency is largely a ceremonial post, but plays a key role with a fragmented electorate often throwing up precariously placed coalition governments.
Around 4,500 MPs and state legislators were eligible to vote in the election.
Mrs Patil will succeed A P J Abdul Kalam, a popular missile scientist, as president.
The President-elect when she was still the Governor of Rajasthan.
Pratibha Patil has won the 12th Presidential Elections of the Republic of India, becoming the first woman president of the second most populous country in the world.

Patil, 72, previously governor of the state of Rajasthan, had support from the governing coalition. She won approximately two thirds of the vote, almost double the number of votes of her nearest rival Bhairon Singh Shekhawat, who resigned as Vice-President after losing the poll.

Patil was a last-minute candidate who appeared when the coalition that leads the congress and the communist allies could not choose a common candidate. The supporters of Patil hope that her election could bring to the spotlight, problems that affect women in India, such as the high murder rate or domestic violence and abuse.

More than 4,500 members of the Parliament of India and state Legislative Assemblies were eligible to vote for the largely ceremonial office.

Patil was recently the centre of controversy after allegations that a bank gave out cheap loans to her relatives, and for her controversial statements about the Muslim veil.

The President-elect will succeed the 11th President of India, Dr. A.P.J. Abdul Kalam, an engineer and scientist. She is expected to be sworn in on July 25 in the Central Hall of Parliament.

The President of India, also called Rashtrapati, is the head of state and first citizen of India and the Supreme Commander of the Indian armed forces. The President's role is largely ceremonial. The powers of the President of India are comparable to those of the monarch of the United Kingdom. The real executive authority in India is vested in the Council of Ministers, headed by the Prime Minister. In 1966, Indira Gandhi became the first and to date the only female prime minister of India.