The woman, known as Shishy, was the handmaiden, sexual partner and second-in-charge of Swami Akhandananda at the Satyananda Yoga Ashram on NSW's Central Coast during the 1970s and 1980s.
Shishy told the child abuse royal commission on Friday that starting a sexual relationship with the boy, codenamed APQ, when she was 25 was "the most shameful thing in my life".
She said she was instructed by Akhandananda to start initiating the boy the same way the guru had been having sex with under-age girls on the ashram.
"It's one of the things I really resent Akhandananda for," Shishy said.
However, the commission heard Shishy continued a sexual relationship with the boy after she left the ashram in 1985.
The pair later had a child together and the boy lived in her house.
Under questioning, Shishy, now in her 50s, said she did not want to start the relationship with APQ and did so only on Akhandananda's orders.
But in 1989, after doing a "mind mash program", she realised she was in love with him.
The commission heard Shishy gave evidence in court against Akhandananda on child abuse charges, but didn't tell detectives about her relationship with APQ.
Early in the day's proceedings, Shishy broke down as she told the commission she was sorry for her actions at the ashram.
Witnesses who were children at the Mangrove Mountain ashram have testified that Shishy beat them.
Shishy also admitted she was present when Akhandananda had sex with two underaged girls at the yoga centre, but said she didn't fully appreciate his actions were wrong at the time.
She said she couldn't recall an event one witness told of, where she allegedly lined children up from youngest to oldest and slapped them.
She also said she couldn't recall other alleged abuses.
However, she accepted she slapped children "very hard" and her physical discipline became more extreme as the children grew into teenagers.
The yoga devotee, who produces chanting CDs, said she had no power at the ashram, despite accepting she was the second-in-charge.
She broke down as she said she accepted she had caused significant trauma to children who worshipped her.
"I deeply, deeply regret and feel quite desperately sorry for anything that I did or that I didn't do," she said.
The commission heard Akhandananda began a sexual relationship with Shishy at an ashram in Bondi in 1974, when she was 16.
He told her she was "a very advanced being" and "a chosen one" and she believed him, she said.
The relationship became progressively more violent and Akhandananda's acts more sexually perverse, she said.
Akhandananda was jailed in 1989 for indecent dealings with four girls, but was released when the High Court overturned the conviction in 1991. He died six years later.
The hearing continues on Monday.
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