Rampal was Wednesday whisked away in an ambulance by police.
The deaths of five women and an infant occurred during a stand-off and violent clashes between the controversial sect leader's followers and the security forces.
Senior police officers and Central Reserve Police Force (CRPF) personnel and Haryana Police entered the ashram complex Wednesday evening and Rampal was arrested just after 9 p.m.
"We have arrested him. He is in our custody. He is being taken to hospital for medical examination," a senior police officer said outside the ashram.
"He will be produced in the relevant court tomorrow (Thursday)," he said.
Police sources said Rampal would be taken to Chandigarh after medical examination. He is likely to be presented in a court there Thursday.
There was not much resistance offered by Rampal's supporters and his private army when he was finally taken into custody after 9 p.m., a police officer told IANS.
Sources said Rampal's face was covered with a cloth when he was brought out from inside the ashram.
"The mission (to arrest) has been completed successfully," said Jawahar Yadav, officer on special duty (OSD) to Haryana Chief Minister Manohar Lal Khattar.
Nearly 14,000 followers Wednesday came out of the ashram near Barwala town, 210 km from Chandigarh, even as Rampal continued to evade arrest.
Rampal's key aides, including his relative Purshottam Dass, and spokesman Raj Kapoor were earlier taken into custody, police said.
At least 450 supporters, including private commandos, were also arrested.
Unlike Tuesday's violent clashes between sect followers and security forces, no clash took place Wednesday.
However, tension mounted Wednesday evening as agitated villagers near Barwala, who are opposed to the sect leader, set some vehicles parked nearby on fire.
Earlier, Haryana Police chief S.N. Vashisht told the media in Chandigarh that bodies of four women were handed over by Satlok Ashram authorities to police Wednesday.
One woman, who had a heart ailment, and an 18-month-old child, reportedly suffering from jaundice, died in hospital due to lack of timely medical care, he said.
The director general of police (DGP) said none of the victims bore any bodily injuries.
He said the exact cause of their death would be known only after post-mortem examination.
"Police did not fire a single shot in the whole operation," the DGP said.
Police sources said Rampal and a private army of volunteers were holding followers hostage inside the premises. "They were using women and children as shields," a police officer said.
Fearing more police action Wednesday after Tuesday's clashes left nearly 300 people, including 110 policemen injured, the followers stranded inside the ashram started leaving. The ashram management had claimed that Rampal was not inside the complex.
District authorities said over 10,000 people, who were inside the ashram complex for the past few days, started leaving early Wednesday after a portion of a 20-feet-high wall of the 12-acre ashram complex was brought down.
Police have booked Rampal - who is already facing charges of murder, inciting mobs and contempt of court - for sedition.
He has also been booked for attempt to murder, criminal conspiracy, illegal detention, rioting and preventing government servants from performing duties, the DGP said.
"Police have shown a lot of restraint since yesterday (Tuesday) and have not fired a single shot," Haryana's Additional Chief Secretary (Home) P.K. Mahapatra told the media.
Supporters of Rampal Tuesday clashed with security forces to prevent them from entering the ashram premises. The area around the ashram resembled a battlefield as sect supporters resisted police action.
Sect followers fired at police, lobbed petrol bombs and acid pouches, besides hurling stones and bricks outside the ashram, clearly indicating that the sect was well prepared to resist the security forces.
The sect leader has been avoiding arrest and failed to appear before the Punjab and Haryana High Court although non-bailable warrants were issued against him Nov 5.
Rampal's supporters had indulged in vandalism in a court in Hisar in July when he was going there in connection with a 2006 murder conspiracy case. The high court took suo motu notice of the incident and summoned Rampal.
Khattar, who has otherwise avoided much comment on the Rampal issue, Wednesday tweeted: "Serious charges of sedition against Rampal & several followers by Haryana Police."
"Govt. & Police are committed to ensure strict compliance of High Court orders, priority is to uphold the law without loss of innocent lives," he wrote in another tweet.