Ms von der Leyen put forward a proposal for an initial 30-day ban which could be extended.
The move would have to be approved by leaders of the EU's 27 members, but would not apply to UK citizens.
Addressing a nearly empty press room alongside European Council President Charles Michel, Ms von der Leyen said: "The less travel, the more we can contain the virus."
The commission chief said she was proposing a "temporary restriction on non-essential travel to the European Union," adding: "These travel restrictions should be in place for an initial period of 30 days which can be prolonged as necessary."
She told a press conference: "UK citizens are European citizens so of course there are no restrictions for the UK citizens to travel to the continent."
Coronavirus: Everything you need to know:
Ms von der Leyen said the world was facing "a global health crisis" which would have a "severe impact" on both people and economies.
The proposed ban on travel to the EU would have exemptions for long-term residents, family members of EU nationals and diplomats.
Doctors, nurses, care workers and experts tackling the coronavirus pandemic would also be spared from the ban, Ms von der Leyen said.
As would the transport of goods and frontier workers who commute across the EU's borders.
Ms von der Leyen described the coronavirus pandemic as a "global storm".
In a statement posted on YouTube President von der Leyen said "we have to make sure that we maintain the flow of goods" while still protecting people amid the outbreak.
She added: "Here in Europe, we are heavily affected by the virus".
On Monday Spain became the fourth most-infected nation across the globe as the number of coronavirus cases in the country surpassed that of South Korea.
Downing Street said alternative ways to hold the talks between the UK side led by David Frost and the EU’s team led by Michel Barnier were being examined.
"We continue to hold discussions with the EU on seeing if we can find a way of facilitating the talks to take place, such as teleconferencing," the Prime Minister’s official spokesman said.