Nupur Sharma's comment triggered clashes in Uttar Pradesh.
The BJP on Sunday suspended party spokesperson Nupur Sharma and expelled her colleague Naveen Kumar Jindal over their comments on Prophet Muhammad that have provoked a massive backlash and violence, after saying it "strongly denounces insult of any religious personalities".
"During the thousands of years of the history of India, every religion has blossomed and flourished. The Bharatiya Janata Party respects all religions. The BJP strongly denounces insult of any religious personalities of any religion," it said in a statement earlier in the day.
"The Bharatiya Janata Party is also strongly against any ideology which insults or demeans any sect or religion. The BJP does not promote such people or philosophy," it said.
"India's Constitution gives the right to every citizen to practise any religion of his/her choice and to honour and respect every religion," the party said.
"As India celebrates the 75th year of its Independence, we are committed to making India a great country where all are equal and everyone lives with dignity, where all are committed to India's unity and integrity, where all enjoy the fruits of growth and development," it added.
Later, it released orders suspending Nupur Sharma, pending an inquiry, and expelling Naveen Kumar Jindal. While Nupur Sharma was a national spokesperson for the party, Naveen Jindal led the party's Delhi media unit.
Soon after the suspension, Nupur Sharma posted a statement on Twitter. "I had been appearing on TV debates where Lord Shiva was being insulted every day. In anger, I said something. If my words have hurt anyone's religious sentiments, I withdraw them. My intention was not to hurt anyone," she wrote in Hindi.
Ms Sharma's contentious comment during a TV debate last week, purportedly insulting the Prophet, had triggered a huge outcry and protests from Muslim groups.
As the controversy snowballed, Naveen Kumar Jindal posted a tweet about the Prophet that also angered many, forcing him to delete it.
At least 40 people, including 20 police personnel, were injured during the clashes after two groups clashed on Friday in Uttar Pradesh's Kanpur over a call to shut down markets following the remarks.
One group opposed the shutdown call by the other group, leading to clashes involving incidents of stone-throwing. The police had to fire tear gas shells to disperse the crowd and prevent further violence. The police have arrested 36 people and filed cases against 1,500.
Prime Minister Narendra Modi and President Ram Nath Kovind were at a function 80 kilometres away from the spot when the clashes broke out.
Nupur Sharma has also been named in multiple police cases in Maharashtra over her comment. She initially denied any wrongdoing and claimed that she has been receiving death threats.
The BJP's clarification came on a day when a wave of anger in Arab nations against the comments by the spokespersons of India's ruling party spilled onto social media with trending hashtags and calls for a boycott of Indian products.