On Monday, Juncker expressed "deep regret" at the decision and revealed he had tried to persuade Hill to stay on.
Hill, responsible for financial stability, financial services and the capital markets union, informed Juncker of his decision to resign from his post at the weekend.
The portfolio will now be taken up by Commission Vice-President Valdis Dombrovskis.
Hill said, "Like many people here and in the UK, I am obviously very disappointed about the result of the referendum. I wanted it to end differently and had hoped that Britain would want to play a role in arguing for an outward-looking, flexible, competitive, free trade Europe. But the British people took a different decision, and that is the way that democracy works.
"As we move to a new phase, I don't believe it is right that I should carry on as the British commissioner as though nothing had happened. In line with what I discussed with the President of the Commission some weeks ago, I have therefore told him that I shall stand down.
"At the same time, there needs to be an orderly handover, so I have said that I will work with him to make sure that happens in the weeks ahead."
In an interview with the FT on Saturday, Hill warned that the City of London should brace itself for a new era where its rule book reflects Franco-German interests unchecked by "the British voice."
Hill laid out the imminent shift in power on European rulemaking, which he said could leave British financial institutions bending to Eurozone-dominated priorities, even if London is outside the single market.
Hill's departure is said to be the most tangible sign of British political influence in Brussels evaporating, after its referendum vote seeping from Britons in the EU institutions and the European Parliament. No new British Commissioner has yet been nominated and there are doubts that one will be.
In a statement, Juncker said: "It is with great regret that I have accepted Lord Hill's decision to resign from the Commission. Lord Hill is an experienced politician for whom I have great respect and I want to sincerely thank him for his loyal and professional work as a member of my team.
"At the beginning of this Commission's mandate, I wanted the British Commissioner to be in charge of financial services, as a sign of my confidence in the UK's EU membership of the European Union."
Juncker went on, "To my great regret, this situation is now changing. I have tried to convince Lord Hill to stay on as Commissioner. I consider him to be a true European and not just the British commissioner. However, I understand his decision and I respect it."
He added, "The work of the EU must go on."
He said Dombrovskis was already coordinating many of the key files under the portfolio, working closely with other Commissioners, the European Parliament and the Council on several important legislative proposals in this area, such as the European deposit insurance scheme.
"With his experience, expertise and his good network amongst MEPs, finance ministers and Prime Ministers, he is ideally placed to ensure continuity in the financial stability, financial services and capital markets union portfolio."