She said: "I feel so honoured and I am overwhelmed".
But despite her promises for greater gender equality, von der Leyen did not mention abortion or LGBTi rights in her opening speech. She won 383 votes, compared to the minimum of 374 votes necessary, in a secret paper ballot - only nine more than the required minimum.
The centre-right defence minister will replace Commission President Jean-Claude Juncker on 1 November.
Charles Michel, Belgium's caretaker prime minister and the future president of the European Council also took to Twitter to offer his support, saying he was "looking forward to cooperate closely with the institutions for the future of Europe".
Ursula Gertrud von der Leyen needs the support of an absolute majority of European deputies.
Martin Selmayr, the German controversial secretary general of the commission, announced he would resign in accordance with Brussels tradition that dictates no two people of the same nationality can hold the EU's executive's most powerful posts.
Parliament now comprises 747 MEPs as per the official notifications received by member state authorities, so the threshold needed to be elected was 374 votes, i.e. more than 50% of its component members.
In Brussels EU officials and diplomats said they were reserving judgment but are now increasingly braced for a "no deal" at the Halloween deadline.
"This is about much more than a personnel issue", senior Social Democrat MEP Katarina Barley told ZDF television.
He added: "In some ways I'm really rather pleased, because you have just made Brexit a lot more popular in the United Kingdom, thank God we are leaving". "We think it is very important that the Council can not simply throw that in the trash with loud applause from right-wing populists".
The ECR has promised to be "pragmatic" and concerned officials admit it might be members hostile to closer European Union integration that get von der Leyen over the line.
She had faced something of an uphill battle in the European Parliament, having been put forward as a compromise candidate after lackluster election results for the traditionally powerful center-right and center-left made it hard to gain enough support for either of the candidates they had put forward before the May vote.
She then immediately addressed what she sees as the biggest challenge: climate change.
Ursula von der Leyen, who was confirmed as the first woman president of the European Commission in Strasbourg on Tuesday, said she would support a Brexit extension but warned the Withdrawal Agreement would not be renegotiated.
At the same time, the pan-European political groups that came together after the vote are frustrated by the way von der Leyen's candidacy was foisted on them.
"If she becomes the first woman to lead the European Commission, that will make her proud, but she won't see it through the gender perspective but from the point of view of a politician who wants to solve the real problems".
In Strasbourg, Nigel Farage, the Brexit Party leader, accused Mrs von der Leyen of wanting to build "a centralised, undemocratic, updated form of communism where nation state parliaments will cease to have any relevance at all".
In addition, she reiterated previous proposals to extend the EU emissions trading scheme (ETS) to more industries and introduce a carbon border tax to help ensure a level playing field for European emitters.
In 2013, von der Leyen was appointed Germany's first female defence minister, but problems involving failing army equipment and shortcomings within military training quickly saw her popularity plummet.