Note: The following article contains discussion of themes including suicide that some readers may find upsetting.
The graphic moment takes place in the final episode of the first season, depicting Hannah Baker (Katherine Langford) taking her own life in her bathroom.
However, it has now been altered to only show Hannah staring in the mirror before cutting to her parents' reaction to her death in a later scene.
In a statement, Netflix said: "We've heard from many young people that 13 Reasons Why encouraged them to start conversations about difficult issues like depression and suicide and get help — often for the first time.
"As we prepare to launch season three later this summer, we've been mindful about the ongoing debate around the show.
"So on the advice of medical experts, including Dr Christine Moutier, Chief Medical Officer at the American Foundation for Suicide Prevention, we've decided with creator Brian Yorkey and the producers to edit the scene in which Hannah takes her own life from season one."
Showrunner Yorkey added: "It was our hope, in making 13 Reasons Why into a television show, to tell a story that would help young viewers feel seen and heard, and encourage empathy in all who viewed it, much as the bestselling book did before us.
"Our creative intent in portraying the ugly, painful reality of suicide in such graphic detail in season one was to tell the truth about the horror of such an act, and make sure no-one would ever wish to emulate it.
"But as we [get] ready to launch season three, we have heard concerns about the scene from Dr Christine Moutier at the American Foundation for Suicide Prevention and others, and have agreed with Netflix to re-edit it.
"No one scene is more important than the life of the show, and its message that we must take better care of each other. We believe this edit will help the show do the most good for the most people while mitigating any risk for especially vulnerable young viewers."
The Netflix series has attracted controversy for its depiction of suicide ever since it first launched over two years ago.
Most recently, a study found that teen suicides rates had risen following the show's release, though the show hit back and argued that 13 Reasons Why had helped puncture the stigmas surrounding anxiety, suicide and depression.
13 Reasons Why seasons 1 and 2 are available to watch on Netflix.
We would encourage anyone who identifies with the topics raised in this article to reach out. Organisations who can offer support include Samaritans on 116 123 (www.samaritans.org), and Mind on 0300 123 3393 (www.mind.org.uk). Readers in the US are encouraged to contact the National Suicide Prevention Lifeline on 1-800-273-8255 or visit the American Foundation for Suicide Prevention.
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