"The TCA marks the foundation of a strong and close partnership with the UK. Faithful implementation is essential," she said in a tweet.
British Prime Minister Boris Johnson said this week was the final step in a long journey, providing stability to Britain's new relationship with the EU.
"Now is the time to look forward to the future and to building a more global Britain," he said in a statement.
The lawmakers also voted massively in favour of an accompanying resolution in which they describe Brexit as a "historic mistake".
The text talked of the trade deal's limited scope, with opportunities for Britain's largely service-based economy "vastly reduced".
Lawmakers condemned Britain’s unilateral change in trading arrangements in Northern Ireland and urged the Commission to press on with its legal action.
They also warned the European Union to be vigilant about British action on taxation, money-laundering and access for EU fishing boats to its waters.
Britain left the EU at the end of January 2020, but remained in the EU single market until the start of 2021. The deal struck in December ensures zero tariffs and quotas, but adds new checks and paperwork that hinder trade.
British exports to the EU fell by 47% in January-February and imports by 20%, far more than the declines for any other EU trading partner.
EU lawmakers see the trade deal, including potential sanctions such as closing market access, as a tool to keep Britain in check.
Christophe Hansen, one of the lawmakers in charge of the file, said the vote should be seen more as an insurance policy.
“Ratification of the agreement is not a vote of blind confidence in the UK government’s intention to implement our agreements in good faith,” he said.