Paris will be the new host of the European Banking Authority (EBA), while Amsterdam will host the European Medicines Agency (EMA), both of which will relocate from London after the UK leaves the European Union.
The EMA and the EBA currently employ about 1,000 people in London.
French President Emmanuel Macron tweeted that the win for Paris was "a recognition of France's attractiveness and European commitment".
Ministers from the 27 EU countries remaining in the bloc after the UK departs in 2019 took part in a secret ballot to pick the victors.
Some 16 cities, including Valletta, bid for the EMA, which is seen as the most desirable of the two agencies, but Malta withdrew its candidacy early.
Eight cities – Brussels, Dublin, Frankfurt, Paris, Prague, Luxembourg City, Vienna and Warsaw – vied to host the EBA. Frankfurt, which is home to the European Central Bank, lost out early in the voting. The final vote came down to Paris against Dublin.
"Businesses now need certainty. The best way to do this is by an early agreement to a transition timeframe and continued close regulatory cooperation,” said Steve Bates, chief executive of the UK's BioIndustry Association, quoted by the BBC.
"We must now ensure Brexit does not disrupt the safe supply of vital medicines to tens of millions of families in the EU 27 and the UK."