The video was played at a pro-Trump event in Florida over the weekend, causing significant uproar among the media, The New York Times reported on Monday.
After suspending Donktum's account, Twitter said the problem was copyright violation (reported by Universal Music Group) not the content.
"Reached for comment, a Twitter representative said the company took down the account in response to a complaint from a copyright holder," reports The Verge.
The fake Trump video was created by TheGeekzTeam, a group of creators owned by Donktum. His account was later restored.
Donktum said the video that triggered the copyright takedown was a Super Bowl commercial posted in early February 2018.
"What they told me in the email is that I was suspended for copyright infringement. It was an indefinite or permanent suspension, but it was obviously reversed," he told his followers on Periscope.
Donktum's content has frequently appeared on Trump's Twitter feed throughout his presidency. He also attended the White House's social media summit over the summer.
Google-owned YouTube said that the Donktum video did not violate its content policies and would not be removed.
"For content containing violence that is clearly fictional, we age-restrict and display a warning interstitial. We applied these protections to this video," a YouTube spokesperson was quoted as saying.
( With inputs from IANS )