The French midfielder, signed by the Italian for £40m in the summer, received his marching orders for two quick-fire yellow cards.
Bakayoko had looked out of his depth from the first minute, gifting Watford multiple chances to score.
Chelsea's fans were enraged with his brief performance, aiming abusive songs in the 23-year-old's direction.
The Blues have won just once in their last five Premier League game and time appears to be running out for their boss.
"Two yellow cards in a few minutes, for sure you have to pay attention to avoid this situation," he said after the game.
"It was a difficult moment for us and then to go down 10 men and play with 10 players it wasn't good.
“Two yellow cards in a few minutes, for sure you have to pay attention to avoid this situation”
Antonio Conte
"I didn't see what happened with the penalty.
"We lost the game, I think we started in a bad way. We were very poor."
Chelsea brought on Olivier Giroud for a debut in the second half.
getty
They scored an undeserved equaliser when Eden Hazard curled home brilliantly from 25 yards.
But Watford netted three times in the last 10 minutes to seal a famous win.
The west London outfit are in action next Monday as they host West Brom at Stamford bridge (8pm).