As expected, the motion on Thursday failed to get the two-thirds majority it needed to pass.
Only 175 members of parliament backed the motion, while 360 voted against and 18 abstained.
Romanian nationalist Gheorghe Piperea, the lead sponsor of the motion, had criticised among other things the Commission's refusal to disclose text messages between von der Leyen and the chief executive of Pfizer during the COVD-19 pandemic.
"The decision-making has become opaque and discretionary, and raises fears of abuse and corruption. The cost of obsessive bureaucracy of the European Union such as (tackling) climate change has been a huge one," Piperea told the parliament on Monday.
During the debate on her leadership, von der Leyen defended her record in parliament, rejecting criticism on her management of the pandemic and asserting that her approach ensured equal vaccine access across the EU.
Although the censure motion had little chance of success, it was a political headache for von der Leyen as her Commission negotiates with US President Donald Trump's administration to prevent steep US tariffs on EU goods.
It was the first time since 2014 that a Commission president has faced such a motion.
Then president Jean-Claude Juncker also survived the vote.
