The decision was adopted by 660 votes in favour, five against and 32 abstentions, while the accompanying resolution, setting out the parliament's evaluation of and expectations from the deal, passed by 578 votes, with 51 against and 68 abstentions.
The vote took place on Tuesday, with results announced on Wednesday.
EU and UK negotiators had agreed on the Trade and Cooperation Agreement (TCA) in a last-ditch attempt last December when they established the terms for future EU-UK cooperation.
To minimise disruption, the agreement has been provisionally applied since the beginning of this year and valid until the end of April.
European Commission President Ursula von der Leyen immediately welcomed the news, which brings to an end more than four years of acrimonious negotiations between the two sides.
"I warmly welcome the@Europarl_EN vote in favour of the EU-UK Trade and Cooperation Agreement. The TCA marks the foundation of a strong and close partnership with the UK. Faithful implementation is essential," she wrote on Twitter.
The UK joined the EU bloc in 1973 but announced to withdraw in 2016 after a referendum.
The EU-UK trade in goods has been deeply affected by Brexit, according to latest figures published by Eurostat, the EU's statistical office.
In the first two months of 2021, exports from the bloc to the UK fell 20.2 percent compared to last year, while the EU's imports from the UK recorded an even sharper decrease of 47 percent.
