Pancholi was arrested on Monday after Khan's mother, the 1980s actress Rabia Khan, made public a six-page letter apparently written by the 25-year-old actress before she hanged herself on June 3. Her last phone call was to Pancholi.
In the letter, widely published in the Indian media, the British-educated Khan speaks of being physically and emotionally abused and of having to have an abortion against her will.
As Khan visited her daughter's grave on Wednesday vowing to "fight for justice", Pancholi's mother, the veteran Bollywood actress Zarina Wahab, broke her silence on the scandal, saying her son was not responsible for the actress's death.
"I know the pain that Jiah's mother is going through," Wahab told Mumbai's DNA newspaper, adding the family was in shock that Pancholi could face charges of abetting Khan's suicide.
"But I also know my son. I know what he's capable of doing ... and the behavior that I hear being attributed to him is not like my son at all."
Pancholi, 22, whose father Aditya is also a film actor, appeared in court and was remanded in police custody until June 13 after which police will have to apply for an extension.
Indian media said the authenticity of the suicide letter needed to be verified by handwriting experts.
Khan's suicide and Pancholi's arrest shocked the Indian film industry. Several Bollywood stars attended a prayer meeting for the actress on Saturday.
Khan, whose real name was Nafisa Khan, was found hanged in her room in a Mumbai apartment last week.
The U.S.-born actress made her Bollywood debut in 2007 with Ram Gopal Varma's "Nishabd", playing the 18-year-old female lead opposite one of India's leading actors, Amitabh Bachchan.
"Nishabd" received mixed reviews and did not do well at the Bollywood box office but Khan went on to play supporting roles in two more films, the psychological thriller "Ghajini" in 2008 and the comedy "Housefull" in 2010.
However Khan had not appeared in a movie since 2010 and filmmaker Varma said in a tweet after her death that the actress had been depressed about her stalled Bollywood career.