The surprise choice of German Defence Minister Ursula von der Leyen to replace Jean-Claude Juncker came after the main front-runners were rejected.
IMF chief Christine Lagarde has been nominated as the first woman to head the European Central Bank (ECB).
The announcement follows days of difficult negotiations.
In all, EU leaders were tasked with nominating five people for the top jobs.
Belgian liberal Prime Minister Charles Michel is nominated to replace European Council President Donald Tusk while Spain's Josep Borrell is proposed as foreign policy chief.
The fifth key role - president of the European Parliament - is to be chosen on Wednesday. Possible candidates include German centre-right MEP Manfred Weber and Bulgarian socialist Sergei Stanishev.
Most of the roles must be ratified by the European Parliament.
Is everyone happy with the choices?
"We have agreed the whole package before the first session of the European Parliament," said Mr Tusk.
He said Germany had abstained on Mrs von der Leyen's nomination over coalition issues but pointed out that Chancellor Angela Merkel herself had backed her.
French President Emmanuel Macron said the nominations were "the fruit of a deep Franco-German entente".
"Von der Leyen is a very good candidate and a very good choice to head the European Commission," he told reporters, adding that Ms Lagarde's "capacities and competences... totally qualified her" for the ECB.
Days of indecision reveal EU power shift
Ursula von der Leyen - if confirmed as new European Commission president - will not bring winds of change to Brussels. She's loyal to the German Chancellor Angela Merkel, a true Christian Democrat and a conservative Europhile.
As for Brexit, remember, the European Commission negotiated on behalf of EU member states. Those negotiations ended when the UK government signed off on the Brexit Withdrawal Agreement back in November.
The only ones now with the legal power to change or add to the text are EU national leaders, not the commission. And what these days of indecision among national leaders over these top EU jobs have shown us is that while France and Germany are still powerful, they are not all-powerful in EU circles any more.
Chancellor Merkel and President Macron were unable to impose on others the EU job allocation plan agreed between them at the G20. Something for the new UK prime minister to consider, perhaps, ahead of planning trips to Berlin and Paris to request a renegotiation of the Brexit deal.
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