The measure is expected to lead to higher prices at supermarkets and restaurants, such as pizza parlours and Mexican eateries.
Tomato-based pizza sauces and salsas are among the products likely to be most hit.
About 70% of tomatoes consumed in the US are imported from Mexico, according to advocacy group Florida Tomato Exchange.
Backers of the newly imposed tariff argue that it will encourage consumers to buy tomatoes grown in the US, thereby boosting local trade.
But the Mexican economy and agriculture ministry said it would be “impossible to substitute Mexican tomatoes” given the volume imported from Mexico.
The Mexican government said it would try to negotiate a new deal before its producers were hit, but also promised to help Mexican tomato growers find new markets.
US tomato growers first petitioned the US government for help in 1996, arguing that they were being undercut by Mexican growers, whom they accused of dumping their tomatoes in the US at a price lower than their normal value.
In order to protect its tomato growers, the US issued an antidumping order, imposing duties on imported tomatoes in order to make US tomatoes more attractive to consumers.
Since then, the two countries have signed five agreements which suspended those tariffs in exchange for Mexico agreeing to sell their tomatoes at or above a minimum price.
It is the latest of these suspension agreements – signed in 2019 – that the US has now withdrawn from.
The US president has also threatened to impose 30% tariffs on all Mexican goods from 1 August.
Trump said this was because Mexico, in his view, had not done enough to stop North America becoming a “Narco-Trafficking Playground”.
Other countries, such as Brazil and China, as well as the EU trading bloc have also been threatened with US tariffs.