The resignation comes after one of Porter's ex-wives, Colbie Holderness, a senior analyst for the USA government, provided the DailyMail.com with a photo of herself with a blackened eye.
"I took the photos given to the media almost 15 years ago and the reality behind them is nowhere close to what's being described", the statement reads.
Kelly himself faced criticism for defending Porter only to belatedly reverse course hours after the publication of photos showing one of the ex-wives with a black eye.
His departure will not be immediate in order to facilitate a smooth transition, Sanders said.
His second wife said she filed and received an emergency protective order against Porter.
According to her complaint, Porter left only after she had asked him to leave several times, and he returned minutes later and "punched in the glass on the door", and tried to get into the apartment.
Sanders also described Porter as "someone of the highest integrity and exemplary character".
"I can't say enough good things about him", Kelly said. He is a friend, a confidante and a trusted professional.
Porter just resigned after being accused by both of his ex-wives of domestic abuse.
11 minute scoring drought dooms Illini in loss to Ohio State
These guys knew they were going to have to step it up and we were going to have to have a big match or two, like Cassar. I don't know if Ohio State can sweep the whole state of MI this season, but they do have a good shot at doing so.
She also confirmed a blog post she wrote previous year that detailed her abusive relationship without naming Porter.
Porter denied the accusations but said he was stepping down, although it's unclear when he will leave. "Domestic violence in any form is abhorrent and unacceptable".
White House staff secretaries play an important role in the West Wing, though the position has varied in stature.
Neither Porter nor Hicks were present in a Wednesday morning senior staff meeting, a White House official said. If any other administration had such a high-level staffer accused of beating multiple women, it would have been a scandal that lasted for days or weeks. Hatch's office provided the statement to the White House - at its request - before the Daily Mail story was published.
Mr Porter's White House role involved working with the president and his chief of staff John Kelly. "The president and chief of staff have full confidence in his abilities and his performance".
Holderness, 37, told the Daily Mail that Porter started abusing her after their marriage in 2000.
Holderness, Porter's first wife, described him as "verbally, emotionally, and physically" abusive.
But when the allegations first emerged against Porter, a number of senior aides rallied around him.
White House officials and Republican lawmakers expressed shock at the news.
Mr Porter, well-liked throughout the White House, lost internal support once the photos came out.