A spokeswoman for EU diplomatic chief Josep Borrell confirmed the change was made at the request of the Chinese foreign ministry but defended the decision to go ahead with publication regardless.
"We regret that this joint op-ed was not published in full by the China Daily," Virginie Battu-Henriksson told reporters in Brussels.
She said EU officials raised "very serious concerns" about the request to censor the article.
"The EU delegation decided nevertheless to proceed with the publication of the op-ed with considerable reluctance as it considered it important to communicate on very key messages on EU policy priorities," she added, citing climate change, human rights and the global response to the coronavirus.
Borrell said that foreign diplomatic missions in China have to "work under the conditions and within the limits set by the Chinese authorities".
"It is no secret that China is now a state where there is censorship and control of the media," Borrell told reporters.
The article, published to mark the 45th anniversary of diplomatic relations between the EU and Beijing, called for closer relations.
Coronavirus, which has now killed more than 260,000 people around the world, originated in central China late last year.
But Beijing has sought to curtail mentions of the Chinese city of Wuhan as the origin of the virus, according to EU anti-disinformation experts.
The decision to bow to Chinese censorship caused outrage among some European politicians. Norbert Roettgen, the chairman of the German parliament's foreign affairs committee, said he was "shocked not once but twice".
"First the EU ambassadors generously adopt Chinese narratives & then the EU representation on top accepts Chinese censorship of the joint op-ed," he wrote on Twitter.
The European Commission's chief spokesman Eric Mamer insisted the decision to go ahead with publishing the doctored article "did not mean we consider censorship to be acceptable".
The row comes just a fortnight after the EU was forced to deny caving to Chinese pressure to water down a report on coronavirus disinformation. The New York Times said that under pressure from Beijing, the EU had delayed publication of a regular report on disinformation trends last week, and toned down the final version.