The team were forced to play 60 minutes of the clash at Vicarage Road with 10 men as Tiemoue Bakayoko was sent off with a second yellow card on the half-hour mark.
Conte has played down speculation over his future as Chelsea manager, and now Courtois has claimed that the players are very much behind their boss.
"We believe in [Conte] and we believe in our team," the Belgian told the club's official website. "We have two bad results and we just try to get back, regroup and just continue.
"We showed that we wanted to fight even with 10 men and that shows we have character, but when you lose twice like that it is not good and there are questions raised, but we go back to training with the manager, and training well and turn this situation around.
"Obviously we are disappointed with the two results we have had in the last week, obviously it is not good but we have to regroup in training, have heads high and continue the hard work and just continue what we were doing.
"We have now two bad losses but we are a team with the manager, and everyone is positive about that, and we will try to do our best to win next week."
The Blues sit fourth in the league table, but only two points separate third from fifth.