MEPs voted overwhelmingly in favour of increasing the 2014 budget to €136.1 billion, with 480 votes in favour to 119 against and 86 abstentions.
Member states had proposed a 2014 budget of €134.8 billion, 1.06 billion less than the Commission had wanted.
MEPs reversed cuts in funding for international policy initiatives, such as humanitarian aid to the Middle East and Syrian refugees and added funds for the external border control agency Frontex, in the wake of the Lampedusa tragedy
In areas that MEPs believe are vital to boost the economy, such as the digital agenda, research, entrepreneurship and (youth) employment measures, Parliament followed the budgets committee's recommendations to reverse the €629 million payment cuts proposed by EU leaders in July and to top up the budget with an extra €34 million.
The budget will now be discussed in a conciliation committee.
Speaking after the vote, Deputy Minister of Finance Algimantas Rimkūnas, responsible for the EU budget in the Lithuanian presidency of the EU, said that national governments and the European Parliament shared the same key priorities.
"We seek to promote growth and jobs, youth employment. On the other hand, in the Council’s view, we must strive to ensure that the budget allocations are sufficient, but realistic. It is important to comply with the limitations of the Multiannual Financial Framework.
"This is why we are concerned about the proposal by the Parliament to use the Flexibility Instrument and leave no leeway to cope with the unforeseen situations. However, I strongly believe that we will be able to bridge the gap between our positions in the Conciliation Committee," he said.
Barroso warns MEPs EU running out of cash for 2013
Meanwhile, President of the European Commission José Manuel Barroso called on MEPs and European governments to reach a deal on the 2013 EU budget.
Barroso warned that he EU's executive was running out of money and might not be able to pays its bills as of mid-November.
According to the Commission, the current shortfall is due to unexpected low income from European imports duties.
"Please, at least, vote for amending budget 6, if not there will be a rupture of payment, but I am not asking on behalf of the Council; I am asking this on behalf of the Commission. I think it is my duty to call the attention of all the parts of the budgetary authorities, Council and Parliament, about the negative consequences ... But please let's avoid a rupture of payment, that would not be in the interest of the image of the institutions," Barroso said.
Commission spokesman Olivier Bailly rejected suggestions on Tuesday that the funding gap could lead to a "shutdown" such as recently happened in the United States.
But as EU treaties forbid a budget deficit, the Commission urged the Parliament and the Council to quickly agree on the amending budget.
"This is not an EU shutdown. This is not comparable to the US system in any way. The EU will continue to function properly in the coming weeks ... The president of the Commission had a phone conversation with President Schulz yesterday to inform him of the risk we face in terms of payments and the need to find agreement between the Council and the EP," Bailly said.
The Parliament is now due to vote today on whether to approve an extra budget of €2.7 billion.