The minister was earlier defiant and ignored demands seeking his resignation.
"Since I have made a decision to seek justice in a court of law in my personal capacity, I deem it appropriate to step down from office and challenge the false accusations levied against me, also in a personal capacity", Akbar said, quoted by ANI, in a statement.
Political analysts said Akbar's continuation would have hurt the government as it gears up for general elections next year, laying it open to charges of being insensitive to women.
The minister's resignation came after he issued a statement on Sunday denying allegations by women journalists who had worked with him.
Ramani on Monday expressed disappointment over Akbar's statement, saying that it paid no heed to the "trauma and fear of the survivors" and that she was ready to fight the allegations of defamation.
"It is created to push women back into silent compliance and will silence the voices of the many who have not yet spoken up", it said. Akbar, Akbar tendered his resignation on Wednesday and said he would challenge the accusations against him in a personal capacity.
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He also praised Turkish efforts to set up a demilitarized zone in Syria's province of Idlib. He said that "Turkish partners are doing all they can to fulfill their obligations".
Akbar has filed a defamation suit against her.
More than a dozen women have accused M.J. Akbar, a junior foreign minister, of a range of inappropriate behavior during his career as a journalist before entering politics.
In a spontaneous outpouring over the past three weeks, women have shared their stories of sexual harassment at the workplace on social media, particularly Twitter, naming well-known journalists, actors, directors and authors.
Akbar resigned amid a growing view in the BJP that apart from the legal aspects of the allegations, the broader perception over the controversy was damaging.
The Opposition Congress termed the resignation a "vindication of truth" and hailed the women who stood their ground despite the minister's "defamation threat" and the "misuse of power" by the Modi government. "When asked recently why she had not named me, she replied, in a Tweet: "Never named him because he didn't 'do" anything.'", Akbar said. He then edited The Telegraph, The Asian Age and other newspapers and wrote several books of nonfiction, becoming one of the most influential people in the Indian news media.
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"This was long overdue and it was important that Mr Akbar took moral responsibility for his actions and stepped down from his post".