The European Parliament re-elected von der Leyen with 401 votes in favour, 284 against and 15 abstentions, with seven spoiled papers.
She needed 360 votes to be re-elected.
It had been uncertain until the vote which way the FdI MEPs would go.
Recently, FdI MEP Nicola Procaccini said the Conservative ECR group FdI belongs to and which Meloni chairs would give the national delegations within it freedom to choose how to vote.
The PM was furious that the ECR was left out of the negotiations for the EU top jobs.
There was speculation Meloni might have gotten her MEPs to vote for von der Leyen if she got policy concessions and Italy were given a Commissioner with an influential post.
Von der Leven had a meeting with ECR representatives this week at which a “structural collaboration” between the group and the incoming executive was ruled out.
Meloni was reportedly looking for the new Commission to adopt a tougher stance on migrants, with special focus given to the Mediterranean.
She was also seeking changes to the Green Deal, with a more gradual approach to the ecological transition her preference.
The Commission chief and the Italian prime minister spoke on the telephone late on Wednesday, sources said.
As expected, Deputy Prime Minister and Foreign Minister Antonio Tajani’s Forza Italia party, which is part of von der Leyen’s European People’s Party party, voted in favour.
Fellow Deputy Prime Minister and Transport Minister Matteo Salvini’s League voted against.
ANSA