Actor's exclusion is third shocker from Vanity Fair issue, which featured an apparent third leg and third hand.
According to The Hollywood Reporter, Franco participated in the Annie Leibovitz photo shoot and interview, but was cut at the last minute.
"We made a decision not to include James Franco on the Hollywood cover once we learned of the misconduct allegations against him," a Vanity Fair spokesperson confirmed.
Ally Sheedy, who worked with Franco in his off-Broadway play "The Long Shrift" in 2014, kicked off the backlash by hinting at some kind of bad experience with the actor and filmmaker, tweeting, "James Franco just won. Please never ask me why I left the film/TV business."
While Sheedy never made an actual accusation against Franco, other women came forward. Violet Paley, who dated Franco, tweeted, "Remember the time you pushed my head down in a car towards your exposed penis." Sarah Tither-Kaplan, one of Franco's former acting students who agreed to play a small part in one of his productions, said Franco added extra scenes that seemed "gratuitous or exploitative."
Both women have since spoken out about their allegations in an interview on "Good Morning America." Paley admitted that their consensual relationship both before and after the alleged incident complicated her story, adding, "I am regretful, I was young, he was a celebrity that I looked up to." Kaplan said Franco "is absolutely not a Harvey Weinstein," and reiterated her main beef: "He created exploitative environments for non-celebrity women on his sets."
Franco previously denied the allegations on "Late Show," telling host Stephen Colbert, "The things that I heard that were on Twitter are not accurate, but I completely support people coming out and being able to have a voice because they didn't have a voice for so long. So I don't want to shut them down in any way."
News of Franco's omission follows the internet freaking out over what many thought looked like an extra leg on Witherspoon on the cover, as well as an extra hand for Oprah Winfrey in another shot.
"Well...I guess everybody knows now...I have 3 legs. I hope you can still accept me for who I am," Witherspoon tweeted in response to the social media chatter. Oprah added in another tweet, "I accept your 3rd leg. As I know you accept my 3rd hand."
Vanity Fair later used humor for damage control about their confusing photoshoot: