Two BJP leaders, Lal Singh and Chander Prakash Ganga, had allegedly put their weight behind the Hindu Ekta Manch in demanding a CBI probe into the Kathua gang-rape and murder case, directly accusing the Crime Branch of an unfair investigation. Both of them have resigned.
The PDP and the BJP are in alliance in Jammu and Kashmir.
Ms Mufti's People's Democratic Party and the BJP had almost reached a breaking point after the two BJP leaders participated in a rally on March 1 to protest against the Crime Branch.
With the two BJP ministers stepping down now, Ms Mufti said a sense of justice had been reinforced in the state. "New Delhi must wake up to the Kashmir cauldron," she said.
On Friday, Prime Minister Narendra Modi had said "such incidents" could not be part of any civilised society, also referring to the rape of a 16-year-old allegedly by a BJP legislator in Uttar Pradesh's Unnao.
Ms Mufti said she was in constant touch with BJP president Amit Shah, BJP general secretary Ram Madhav and home minister Rajnath Singh. "I want to thank people of Jammu for standing united against the gory crime," she said.
The move to placate the PDP came after Mr Madhav flew to Jammu on Saturday morning and met with party legislators, following which Lal Singh and Chander Prakash Ganga were told to resign and Ms Mufti was informed of the decision.
For three days, the accused gang-raped her repeatedly, keeping her sedated and without food. Before she was strangled and hit twice with a heavy rock for good measure, one of the men stopped the killer to rape her one last time, the police said.
The girl's body was found in the forests on January 17.
"The charge that the two ministers were pro-rapist is absolutely wrong. It was sheer indiscretion on their part," Ram Madhav said, adding there was no pressure from the PDP to sack the two BJP ministers.
"As far as this case is concerned, we have done our bit by allaying the fears and misconception created in the minds of not only the people of Jammu and Kashmir but also in the entire country by asking our two ministers to resign. Beyond that, I don't think there will be any impact of this incident or these developments on the coalition."
With inputs from PTI and IANS