The 12 Years A Slave actress posted a picture of the original shot on Instagram alongside the final November front cover, appearing to show her ponytail airbrushed out.
Along with the images, Nyong'o wrote a lengthy message, explaining that she now "embraces her natural heritage" after years of aspiring to "light skin and straight, silky hair" rather than her own "dark skin and kinky, coily hair".
Nyong'o, who was raised in Kenya, said she was "disappointed" in the magazine and could not "condone the omission".
The post notched up more than 150,000 likes in less than 12 hours.
In a statement issued in response to the post, Grazia "apologised unreservedly" to Nyong'o, saying it is "committed to representing diversity throughout its pages".
It added: "Grazia magazine would like to make it clear that at no point did they make any editorial request to the photographer for Lupita Nyong'o's hair to be altered on this week's cover, nor did we alter it ourselves."
The fashion magazine also said it was not aware of all alterations that had been made.
In response to the removal of her arching hoop of braids, Knowles posted the unaltered image to Instagram with the caption "#dtmh".
The hashtag referenced the title of a song on her 2016 album A Seat At The Table - Don't Touch My Hair - written about the tradition of hair braiding and its cultural and artistic importance in history.
The Evening Standard's magazine said they had altered the image "for layout purposes" but admitted they had made the "wrong call".