The verdict against Asaram Bapu, 77, was read out inside a prison in Jodhpur, Rajasthan state, due to fears that his followers might resort to violence.
Security was tight around the prison complex and in states where the guru has a large following.
It is the latest high-profile rape case in India, following others that have fuelled public protests and raised questions about how police handle allegations and treat victims.
In August, another popular guru, Gurmeet Ram Rahim Singh, was sentenced to 20 years in prison for raping two female followers.
Responding to widespread outrage over the recent rape and killings of girls and other attacks on children, India’s government last week approved the death penalty for people convicted of raping children under the age of 12.
The judge, Madhusudhan Sharma, announced the prison term for Bapu and sentenced two of his associates to 20 years in prison each for helping him in the crime. Sharma convicted Bapu on charges of criminal conspiracy, wrongful confinement and rape.
Bapu has denied the charges, and a spokesman said he would appeal against the verdict in a higher court.
In her complaint to police in 2013, the girl accused Bapu of raping her when she visited his retreat in Jodhpur with her mother. She was 16 at the time. Her family said they had been followers of Bapu for more than a decade.
Bapu has been in prison since his arrest in 2013. He ran more than 230 ashrams with residential schools with millions of followers across India and abroad, including the US, UK, Canada, Uganda and Kenya.
Religious sects wield considerable political clout in India. Bapu is on trial with his son Narayan Sai in a separate case in which two sisters have accused them of sexual assault.
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An Indian spiritual guru who claims to have millions of followers worldwide has been found guilty of rape.
A court in the northern city of Jodhpur ruled that Asaram Bapu,77, raped a 16-year-old girl in 2013 at his ashram there. He is likely to appeal the verdict in a higher court.
The guru, 77, has 400 ashrams around the world where he teaches meditation and yoga.
He is also standing trial in another rape case in Gujarat state.
Jodhpur city is on high alert because of anticipated violence from the guru's followers.
The security measures come after followers of another guru, Gurmeet Ram Rahim, ran amok after he was found guilty of rape last year. The resulting violence killed 23 people.
What is the case against him?
Asaram was arrested in 2013 after a case of sexual assault was filed against him by two of his followers who alleged that he had assaulted their daughter.
Police say that the couple, who had sent their daughter to one of his Ashrams for spiritual lessons, were summoned to see her as she was "under the influence of some supernatural ghostly powers".
They were then told to take their daughter to Jodhpur to meet the guru.
The family reached Jodhpur ashram on 14 August. The following night, Asaram called the victim to his room on the pretext of "curing" her. He then raped the victim while her parents waited outside chanting his prayers, police say.
Police say the guru forced the victim to perform sexual acts on him and threatened to murder her family if she spoke about the incident.
The victim told her parents what had happened the following day. They tried to confront Asaram, but were refused entry to his ashrams.
Who is Asaram Bapu?
Asumal Harpalani was born in April 1941 in a village called Bernai in the Sindh region in present day Pakistan.
His family migrated to Ahmadabad city in Gujarat after the partition of India.
In the 60s, he started practising spiritualism with different gurus - one of whom gave him the name Asaram.
In 1972, he formed his first ashram on the banks of Sabarmati river in Motera town of Gujarat.
His influence spread to different parts of India and around the world in the following decades.
According to his website, he has 40 million followers around the world.
Important Indian politicians, including Prime Minister Narendra Modi, have attended his sermons in the past.
He also has properties worth millions of dollars across India. The police are also investigating him for corruption and forgery.
Controversies around his trial
Asaram is also accused of raping another woman in Surat city of Gujarat between 2002 and 2004. The trial in this case is underway.
At least nine witnesses in both cases have been attacked over the past five years - three of them have since died.
Police are investigating these attacks.
The victims' families insist that the guru and his followers are behind these attacks - an allegation he denies.
The Jodhpur rape case, for which he has been convicted, has also seen the victim's family threatened by his followers.
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