Twitter's move on Tuesday marks the first time the technology company has sanctioned Trump as criticism mounts about how the president has amplified misinformation to more than 80 million followers on the social media platform.
Trump responded by accusing Twitter of stifling free speech.
Twitter spokesman Trenton Kennedy told NPR that while the tweet about mail-in voting does not violate Twitter's rules since "it does not directly try to dissuade people from voting," it does contain "misleading information about the voting process, specifically mail-in ballots."
The action is the latest confrontation between Washington and Silicon Valley with a presidential election just months away.
Brad Parscale, Trump's 2020 campaign manager, suggested Twitter was attempting to impinge on the president's free speech rights and accused the company of being anti-Trump.
"We always knew that Silicon Valley would pull out all the stops to obstruct and interfere with President Trump getting his message through to voters," Parscale said. "Partnering with the biased fake news media 'fact checkers' is only a smoke screen Twitter is using to try to lend their obvious political tactics some false credibility. There are many reasons the Trump campaign pulled all our advertising from Twitter months ago, and their clear political bias is one of them."
Earlier this month, Twitter announced a move to combat the spread of misinformation about the coronavirus. Twitter said it will place labels on misleading or disputed information about the virus "regardless of who the speaker is."
Critics of Twitter have complained that it has placed Trump above its attempts to enforce rules aimed at making the platform more civil.
Tuesday's action allowing users to "get the facts" about what Trump was tweeting comes just as the social media platform faces criticism for its inaction on a tweet Trump sent advancing a groundless conspiracy theory about the death of an ex-staffer of Joe Scarborough, a former congressman who is now a television host on MSNBC and frequent Trump target.
On Twitter, Trump pushed the baseless theory that Scarborough killed Lori Kaye Klausutis, 28, who was found dead in Scarborough's congressional office in Fort Walton Beach, Fla., in July 2001.
"There has been a constant barrage of falsehoods, half-truths innuendo and conspiracy theories since the day she died," widower Timothy J. Klausutis wrote last week to Twitter CEO Jack Dorsey. "... Because of this, I have struggled to move forward with my life."
He went on to ask Dorsey: "My request is simple: Please delete these tweets,"
Despite the plea, Twitter has not removed the tweet advancing the false conspiracy theory about the death of Klausutis' wife, who had an undiagnosed heart condition, passed out and hit her head on her desk when she fell. Dorsey never directly replied to the widower's letter.
But in a statement, Kennedy, the Twitter spokesman, said the tweets about Scarborough do not violate company policies.
"We've drawn lines for certain issue areas, including civic integrity and voting," Kennedy said. "However, as we said on the Scarborough tweets, we've been working to expand existing product features and policies so we can more effectively address things like this going forward, and we hope to have those changes in place shortly."
Twitter, which has some 330 million users, has had a longstanding practice of exempting world leaders from its content rules under a "newsworthiness" exemption. But the pandemic has caused it to revamp its policies.
Twitter officials now say posts by any user, even world leaders, are subject to carrying warning labels, or being removed altogether, if the content runs afoul of the guidance of leading public health agencies.
And it has made good on that promise by deleting tweets by Brazilian President Jair Bolsonaro and Venezuelan President Nicolás Maduro.
Bolsonaro praised the use of anti-malaria drug hydroxychloroquine and called for an end to social distancing. And Maduro promoted a "natural brew" to remedy those infected with COVID-19.
Twitter said such posts violated its policies, but the company has never deleted a tweet by Trump.