The music producer called the film "disrespectful" and the reason why "people should never remake movies".
The 42-year-old, who worked closely with the singer before her death in 2001, criticised the Lifetime biopic during its airing on Saturday.
One message warned the film's producers that they will "feel [his] wrath tomorrow morning".
Much of the criticism centred around the film's casting.
Many fans felt Izaak Smith and Chattrisse Dolabaille who played Timbaland and Missy Elliot in the film, were called too thin and fair.
Others were more angry at the network's "romanticising" of Aaliyah's relationship with R Kelly.
The pair reportedly married illegally when Kelly was 27 and Aaliyah was just 15.
Aaliyah: The Princess Of R&B has had troubles long before its airing at the weekend.
Aaliyah's family didn't allow the studio to use her music, and Zendaya Coleman, who was originally picked to play the Rock The Boat singer, backed out after describing the project as "rushed".
But executive producer Debra Martin Chase insisted the team tried to keep the movie tasteful.
"Biopics are hard," Chase told the Washington Post.
"People have an opinion and social media allows them to voice that opinion. But at the end of the day, our goal was to make the best movie possible."
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Timbaland has slated the new Aaliyah biopic in a series of pictures and memes posted on his Instagram page.