Carneiro had claimed constructive dismissal by the Premier League club and sexual discrimination by Mourinho, who she alleges abused her on the opening day of the Premier League season
last August after she had entered the field of play to treat Eden Hazard.
Mourinho had labeled the club's medical staff "naive" for treating Hazard with his team already down to 10 men. Carneiro
was dropped from first-team duties after the contest and left the club six weeks later.
The Portuguese coach, now in charge of Manchester United, was fired four months after the incident.
A statement from Chelsea read:
"The club regrets the circumstances which led to Dr. Carneiro leaving the club and apologizes 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.
"Dr. Carneiro has always put the interests of the club's players first. Dr. Carneiro is a highly competent and professional sports doctor. She was a valued member of the club's medical team and we wish her every success in her future career.
"Jose Mourinho also thanks Dr. Carneiro for the excellent and dedicated support she provided as First Team Doctor and he wishes her a successful career."
: What went wrong for Mourinho?
During last season Mourinho was cleared by the English Football Association of making discriminatory comments towards Carneiro, though the Women in Football group said at the time it was "appalled by the conclusion of the FA investigation."
On Monday, it was reported that Carneiro had rejected a $1.7m deal to settle her claims before confidential settlement was reached Tuesday.
"I am relieved that today we have been able to conclude this tribunal case," Carneiro said in a statement.
" 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. In running onto the pitch to treat a player, who requested medical attention, I was following the rules of the game and fulfilling my medical responsibilities.
"I would like to thank everyone who has supported me including my husband, family and friends and members of the football community."
Keep up to date with all the latest football news on CNN
and on our Facebook page.