The 18-year-old had been linked with a number of clubs in this summer's transfer window, but the Hornets have swooped to land him on a four-year contract.
Quina joined West Ham from Chelsea in 2016, and leaves the Hammers having made six first-team appearances - four of which came during the 2017-18 campaign.
"The Hornets are delighted to announce the deadline-day signing of highly-rated Portuguese attacking midfielder Domingos Quina," read a statement on Watford's official website.
"Watford also hold the option on an additional 12 months for the talented Portugal Under-20 international."
The transfer window slammed shut at 5pm, but Watford were granted an extension by the Premier League, which allowed the deal to go through at a later stage.