The European Banking Authority (EBA) will relocate from London to Paris after Brexit.
The French capital defeated stiff competition to win the key agency in a victory Paris will view as a boost to its bid to get banks to shift operations from London after the UK leaves the EU.
EU chiefs had earlier announced they will move the European Medicines Agency (EMA) from London to Amsterdam after Brexit.
The two agencies are currently based in Canary Wharf where they employ around 1,000 staff.
Announcing the decisions, Estonian deputy EU affairs minister Matti Maasikas said the votes for where to relocate both agencies ended in a tie and had to be decided by the drawing of lots.
Paris was tied with Dublin in the battle for the EBA, while Amsterdam received the same number of votes as Milan for the EMA relocation.
Mr Maasikas said: “It was a tight competition, and we needed to draw a lot on both cases.”
Italian prime minister Paolo Gentiloni denounced the decision to award the EMA to Amsterdam by picking names out of a bowl.
Reports suggested that Milan was ahead in the first round of voting, with the backing of 12 EU countries, ahead of nine for Amsterdam and five for Copenhagen.
After the Danish capital was knocked out and its votes redistributed, the result was a 13-13 tie, leaving the Estonian minister chairing the meeting to draw lots to decide a winner.
Writing on Twitter, Mr Gentiloni said: “A solid candidate defeated by a drawing of lots. What a mockery.”
A Government spokesman said the UK would continue to work with both relocated agencies.
“As part of our new deep and special partnership, we want to ensure close collaboration on major science, research and technology initiatives continues. This, of course, includes with the EMA. Our commitment to ensuring patients’ safe and timely access to medicines remains unchanged.
“We are also keen to build a new positive relationship with the European Banking Authority. London is a global financial hub, and we are determined to maintain the sound regulatory framework and global standards that underpin the City’s leading position.”
Liberal Democrat leader Sir Vince Cable said: “While not surprising, these moves mark the beginning of the jobs Brexodus.
“Large private sector organisations are also considering moving to Europe and we can expect many to do so over the next few years.
“That David Davis suggested the UK could keep these agencies shows just how little grasp the Government has of the potential consequences of Brexit.”