"Our team got a tip-off that Sai was on the move from Punjab to Haryana. The team laid a trap and he was arrested from Pipli village near Kurukshetra (in Haryana)," Additional Commissioner of Police (Crime) Ravindra Yadav told IANS.
Sai, 40, who had gone underground after two sisters from Surat filed rape complaints against his father and him at different police stations in Gujarat. The two alleged they were raped by the duo during their stay in the ashram in the mid-2000s.
The 30-year-old woman who filed a complaint against Sai alleged he raped her between 2001 and 2005.
Sai's father Asaram, 72, is in Jodhpur central jail for sexually assaulting a girl, 16, in his Jodhpur ashram of Rajasthan in August. The spiritual leader also played a cat-and-mouse game with the police before he was arrested from Indore Sep 1.
Sai was wearing a saffron headgear, T-shirt, pant and a jacket worn by many Sikhs in Punjab to hide his identity when he was arrested.
Giving details of the arrest, Yadav said a Delhi Crime Branch team intercepted an SUV with an Uttar Pradesh registration number at a refuelling station near Kurukshetra.
Sai, who has been constantly on the move from one city to another, was in the vehicle along with Hanuman, driver Ramesh, Vishnu and Bhavika. The four were also arrested.
"Narayan Sai, who has been accused of sexual assault, will be produced in the Rohini Court at 3 p.m.," said the police officer.
After he is produced in court, the Surat police will take him on transit remand where the FIR has been registered against him.
As Sai was on the run, the Surat police had announced an reward of Rs. 5 lakh. His accomplice Hanuman, also named in the police complaint, carries a reward of Rs.1 lakh.
Sai was in Jaipur when the FIR was registered against him.
He then left for Agra and came to Delhi. He stayed for a week in a ashram at Naimi Saran, Sitapur, Uttar Pradesh, where he changed his looks by getting clean shaven.
He then reached Haridwar through Greater Noida, where he stayed for 10 days at an apartment. He also briefly stayed in Thane (Maharashtra), Gujarat, Udaipur and Rajkori, police said.