The self-styled "godman" urged his supporters against violence and said he would personally appear in court on Friday.
The skyline of Panchkula district near Chandigarh, the capital city of Punjab and Haryana, was covered in thick smoke.
Mobs also set fire to government buildings, and attacked police and TV journalists, smashing the windshields of media vans and breaking broadcast equipment. He faces a minimum of seven years in prison.
He will receive his sentence on 28th August but has been flown over to a Haryana-based jail by helicopter until that date.
Singh's Dera Sacha Sauda sect describes itself as a social welfare and spiritual organisation but he is no stranger to controversy.
Baba Ram Rahim Singh has denied the charges against him.
At least 12 people are dead and many more injured after a guru was convicted of rape in India.
"The followers are still inside the compound and they could be in the numbers of 10,000 and upwards though people are leaving the compound", Vijay Kumar, the Deputy Superintendent of Police in Sirsa, told CNN.
The police and paramilitary forces could not react adequately as the mobs indulged in violence.
Train services were cancelled through the area, leading to delays across northern India, and schools and colleges were closed. An alert was sounded in Uttar Pradesh as well.
He claims a following of more than 60 million devotees worldwide, but stands accused by former sect members of surrounding himself with about 400 castrated bodyguards.
A curfew imposed in Sirsa, where soldiers patrolled empty streets, was briefly lifted yesterday to allow Singh's followers to leave the headquarters. There is no direct parallel between Singh and any individual political or otherwise in Pakistan, but there are parallels in organisational terms - his sect runs campaigns against drug and alcohol abuse, supports sex workers and provides relief, often extensive, in the wake of natural disasters. He (Dera chief) has lakhs of followers in the country and in the state.
Similar violent incidents are also being reported in the neighbouring state of Punjab where Singh's supporters have torched a gas station and a railway station. Gandhi appealed to everyone to maintain peace and harmony.
A close aide of Prime Minister Narendra Modi said central and state officials had been instructed to work round the clock to restore law and order. Vineet Joshi, a Punjab BJP leader, put a counter-question.
Following the outbreak of violence, Haryana Chief Minister Manohar Lal Khattar called an emergency meeting to take stock of the situation.