The Premier League champions were 2-1 down to the high-flying Hornets when Batshuayi replaced Alvaro Morata off the bench, and the Belgian scored twice to help his side turn it around and pick up three important points.
The 24-year-old has made just three Premier League starts since joining Chelsea in the summer of 2016, but Conte believes that it is important for him to wait for his chance.
"Don't forget Michy is a young player. For him this is the first big experience with a great team," he told reporters.
"Today the impact was incredible and important, it must continue in this way - work, work, work, to have the passion to improve and understand he has to wait for his moment and then when he has the chance to show he has improved."
The victory leaves Chelsea fourth in the Premier League table, having leapfrogged Watford into the Champions League places.