Carneiro had claimed constructive dismissal by the Premier League club and sexual discrimination by Mourinho who appeared at the tribunal and sat in the front row.
Terms of the settlement remained confidential.
Carneiro worked for Chelsea for six years until she left in September after clashing with Mourinho in the closing minutes of theopening Premier League match of the seasonagainst Swansea City at Stamford Bridge in August.
The 42-year-old ran on to the pitch with physio Jon Fearn after being called on by referee Michael Oliver to treat winger Eden Hazard.
After the game Mourinho described the pair as "impulsive and naive". Carneiro was relieved of her match-day duties soon afterwards.
Portuguese Mourinho was fired as manager in December.