The 17-year-old reality star used her Twitter account to encourage followers to "spread the love" rather than post critical and hurtful messages about Bruce.
Speaking after Bruce's big interview with ABC News, in which he confirmed he is a woman, she said: "I don't have the time for people who bring and create so much negativity in their life. I can only pray for them!
"There's bigger things than that!!! Spread love! We are all battling something."
Kylie also said: "Woke up still in awe... I've never been more proud of you, Dad!!!!!!"
The Keeping Up With The Kardashians star is Bruce's youngest child. He's also father to Kendall, Brody, Burt, Brandon and Cassandra, as well as being stepfather to Kim, Khloe, Kourtney and Rob Kardashian.
Bruce confirmed rumours of his gender transition on Friday evening, telling Diane Sawyer: "For all intents and purposes, I'm a woman.
"People look at me differently. They see you as this macho male, but my heart and my soul and everything that I do in life - it is part of me.
"That female side is part of me. That's who I am."
The Olympic gold medal winner's four eldest children - Burt, Cassandra, Brandon and Brody - all appeared on the show to support him, while Kylie and Kendall sent a statement saying they loved and supported their father.
All you need to know about Kylie Jenner!
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