Carneiro is suing Chelsea for constructive dismissal and breach of contract, and there is a separate but connected legal claim against Mourinho for alleged discrimination.
Ahead of a first hearing on 6 January, Chelsea filed their defence before the midnight deadline on Thursday.
Mourinho was sacked by the Premier League champions on Thursday.
A date for the full tribunal will be set in the new year, and Mourinho and the Chelsea hierarchy will be compelled to give evidence in person.
Carniero's claim includes a request for reinstatement, raising the possibility of a return to Stamford Bridge for her. However, the club will not be forced to take her back.
She left the club in September after being demoted following criticism from Mourinho of both her and physio Jon Fearn for going on to the pitch to treat Eden Hazard during the 2-2 draw with Swansea on the opening day of the season.
Chelsea were already down to 10 men after goalkeeper Thibaut Courtois was sent off, and with Hazard having to leave the field after being treated despite appearing not to be badly injured, the team were temporarily reduced to nine men.
Mourinho was widely criticised for his comments but was cleared of using discriminatory language by the Football Association.
Carneiro revealed she had not been spoken to personally during the investigation, nor asked to provide any statement, but the FA said she was given an opportunity to do so.
Former Chelsea doctor Eva Carneiro is to continue her legal case against Chelsea and ex-manager Jose Mourinho.