It came after the Government refused to withdraw plans to override key elements of the Brexit divorce settlement.
The two leaders will speak on Saturday to discuss the “next steps” following the conclusion of the final formal round of talks in Brussels.
A No 10 spokesman said: “The Prime Minister will be speaking to President von der Leyen tomorrow afternoon to take stock of negotiations and discuss next steps.”
The chief negotiators Michel Barnier and Lord Frost are also meeting on Friday in the Belgian capital at the end of a week of talks.
Both sides have acknowledged that time is running out if they are to achieve an agreement before the current Brexit transition period comes to an end at the end of the year.
Mr Johnson has said he is prepared to walk away from the negotiations if there is no agreement by the time of the next EU summit on October 15.
Ms von der Leyen said on Thursday that a “letter of formal notification” would be sent to the UK after ministers rejected a demand to withdraw the provisions from the UK Internal Market Bill by Wednesday of this week.
In a press statement at the commission headquarters in Brussels, she said the move marked the first step in an “infringement procedure” with the British Government now invited to send its observations within the month.
“This draft Bill is by its very nature a breach of the obligation of good faith laid down in the Withdrawal Agreement,” she said.
“The deadline lapsed yesterday, the problematic provisions have not been removed, therefore the commission has decided this morning to send a letter of formal notice to the UK Government.
“This is the first step in an infringement procedure. The letter invites the UK Government to send its observations within a month.”
Mrs von der Leyen gave no indication as to what action could follow if the commission did not receive a satisfactory response, although under the terms of the Withdrawal Agreement the EU could take Britain to the European Court of Justice.
A Government spokesman said they would respond to the letter “in due course”.
The Government has argued the Bill – which gives ministers the power override provisions in the Withdrawal Agreement relating to Northern Ireland – is necessary to protect the peace process if there is no agreement on a post-Brexit free trade agreement.
However the move infuriated the EU which accused the UK of violating its treaty obligations after ministers admitted it would breach international law.
Nevertheless, the EU response suggests it is in no hurry to escalate the dispute while talks on a free trade agreement are continuing.
The proceedings adopted by the commission are relatively common, with around 800 open cases against member states last year alone.
Despite the legal action, Downing Street said trade talks with the European Union were being carried out in a “constructive spirit”.
The final formal round of talks will conclude with a meeting between lead negotiators Lord Frost and Michel Barnier on Friday.