Former Chelsea doctor Eva Carneiro has settled her dismissal claim against the club on confidential terms.
Dr Carneiro, who claimed constructive dismissal against Chelsea, also reached a discrimination settlement against the club's former manager Jose Mourinho.
Dr Carneiro said her priority has always been the health and safety of the players.
Chelsea said it apologised "unreservedly" to the former first team doctor for the distress caused.
On Monday it emerged Chelsea had offered Dr Carneiro £1.2m to settle her claims, which she had rejected.
In a statement, Dr Carneiro said: "I am relieved that today we have been able to conclude this tribunal case. It has been an extremely difficult and distressing time for me and my family and I now look forward to moving forward with my life.
"My priority has always been the health and safety of the players and fulfilling my duty of care as a doctor."
Addressing the London South Employment Tribunal centre in Croydon, Daniel Stilitz QC, for Chelsea and Mr Mourinho, said: "We are pleased to be able to tell the tribunal that the parties agreed a settlement on confidential terms."
Dr Carneiro claimed she was sexually discriminated against after she went on to the pitch to treat Chelsea player Eden Hazard during the opening day of the Premier League season last August.
She claimed that Mr Mourinho shouted the Portuguese phrase "filha da puta" at her, which means "daughter of a whore", as she ran on to the pitch.
Hazard had to leave the pitch, briefly leaving the team with only nine men at what Mr Mourinho claimed was a crucial stage in the game.
Chelsea went on to draw 2-2 with Swansea and Mr Mourinho publicly criticised both Dr Carneiro and first team physio Jon Fearn for being "impulsive and naive".
Dr Carneiro left the club in September after being demoted.
Analysis: BBC News correspondent Will Ross
Many will guess but we may never know how much money is winging its way into Dr Eva Carneiro's bank account. She did not accept a £1.2m settlement offer so this was no small business.
It seems bizarre that a dispute that began with a doctor running onto a football pitch to help an injured player would end 10 months later with a flurry of negotiations along the nondescript corridors of a building in Croydon.
Although she will have her critics, this was a major victory for Dr Carneiro who fought for justice in the male dominated world of Premier League football.
Chelsea Football Club would have been keen to avoid the potential embarrassment of a personal feud going even more public.
Jose Mourinho's new employers, Manchester United, would also have been keen to ensure that this did not drag on any longer.
Mr Mourinho will find watching the European Championships better preparation for rebuilding a reputation as a winner than being grilled in Croydon.
As for the public? We had already been treated to the subtleties of swearing in Portuguese. It was time to move on.
Chelsea said in a statement: "The club regrets the circumstances which led to Dr Carneiro leaving the club and apologises unreservedly to her and her family for the distress caused.
"We wish to place on record that in running onto the pitch Dr Carneiro was following both the rules of the game and fulfilling her responsibility to the players as a doctor, putting their safety first.
It added: "Jose Mourinho also thanked Dr Carneiro for the excellent and dedicated support she provided as first team doctor and he wishes her a successful career."
Jose Mourinho leaves the employment tribunal after settling the claims of Dr Carneiro
In a statement to the tribunal, Mr Mourinho - who was sacked by Chelsea in December after a run of poor form - conceded that he used the term "filho da puta", meaning "son of a whore" and insisted he had been using it throughout the match.
But Mary O'Rourke QC, acting for Dr Carneiro, told the tribunal on Monday: "He [Mourinho] uses the word 'filha' because he is abusing a woman."
The FA ruled on 30 September 2015 that the words did not constitute "discriminatory language" after consulting an independent academic expert in Portuguese linguistics.
A spokesman for Women in Football said: "Women in Football are delighted that Eva's name has been rightly cleared and her professional reputation as a doctor upheld.
"Eva has been courageous in her fight for a public apology from Chelsea and acknowledgement that on the day in question she was simply doing her job.
"We completely deplore and condemn her treatment by the club since and welcome their unreserved apology."
Mr Mourinho's presence at the tribunal on Tuesday was unexpected because it was not thought he was going to give evidence until next week.
Also in attendance were Chelsea director Marina Granovskaia, chairman Bruce Buck, head physio Jason Palmer and head of communications and PR, Steve Atkins.
The case was expected to last seven to 10 days and could have led to potentially embarrassing witness statements and documents - including texts and emails - being made public.
Dr Carneiro alleged that on 10 August last year Mr Mourinho told Mr Atkins that he did not want Dr Carneiro on the bench at the next match, adding: "She works in academy team or ladies team, not with me."
She also claimed Chelsea took no action following complaints about sexually explicit chanting at various away games - in particular at Manchester United and West Ham - and a lack of female changing facilities.
Further allegations were that she was not provided with a club suit, and regularly had to endure sexually explicit comments from her colleagues.