The Oscar winner recently took aim at Jessica for wearing a bikini in a photoshoot to accompany a 1999 article, in which the singer talked about the importance of her virginity, explaining it left her "confused".
Simpson took to Twitter on Wednesday, December 05 to respond to the "Black Swan" star, telling Portman she was "disappointed" by her remarks.
"As public figures, we both know our image is not totally in our control at all times, and that the industry we work in often tries to define us and box us in," Jessica wrote. "However, I was taught to be myself and honor the different ways all women express themselves, which is why I believed then - and I believe now - that being sexy in a bikini and being proud of my body are not synonymous with having sex."
She added, "I have made it my practice to not shame other women for their choices. In this era of Time's Up and all the great work you have done for women, I encourage you to do the same."
Portman was quick to apologise, telling Entertainment Tonight her comments were more about mixed messages in the media than about shaming anyone.
"I would never intend to shame anybody and that was absolutely not my intention," Portman says. "I was really talking about mixed media messages out there for young women and completely apologise for any hurt it may have caused, because that was definitely not my intention."
"What I said was I was confused by mixed messages when I was a young girl growing up, and there are a lot of messages for how women should be, and women should be allowed to do whatever they want... It is a mistake to say anyone's name. I could have made my message without naming."