Ye's account showed a notice that it was suspended after one of his posts had earlier appeared to show a swastika symbol inside a Star of David.
The billionaire owner of Twitter, who calls himself a free speech absolutist, had welcomed the return of the rapper, now known as Ye, to the platform in October.
"I tried my best. Despite that, he again violated our rule against incitement to violence. Account will be suspended," Musk tweeted in reply to a Twitter user who said "Elon Fix Kanye Please".
Musk has in the past few months expressed his desire to have fewer limits on content that can be posted on Twitter. He said last week the platform would provide a "general amnesty" to some suspended accounts.
Last month, Twitter reinstated some previously suspended accounts, including that of former US president Donald Trump.
It was not immediately clear if Ye would be allowed back on Twitter and the company did not respond to requests for comment.
Ye, who has more than 30 million Twitter followers, posted a screenshot on Trump's Truth Social platform, showing his Twitter account would be suspended for 12 hours.
The tweet was the latest action by the rapper and fashion designer that has stoked controversy.
On Thursday, Ye praised Nazi dictator Adolf Hitler in an interview with conspiracy theorist Alex Jones on his online Infowars show.
"Ye has arrived in a new ensemble here with us, but I'll assure you it is Ye," Jones said at the start of the interview in which Ye wore a black mask over his entire head obscuring his face as well as black gloves.
Some Republicans condemned Ye's comments.
Iowa US representative Ashley Hinson tweeted "Kanye West's anti-Semitic comments today were disgusting. His pattern of anti-Semitic behaviour is unacceptable and I condemn it in the strongest possible terms."
President Joe Biden also appeared to address the issue in a tweet on Friday:
"I just want to make a few things clear: The Holocaust happened. Hitler was a demonic figure. And instead of giving it a platform, our political leaders should be calling out and rejecting antisemitism wherever it hides. Silence is complicity."
