Carlos Tevez took the plaudits for City in the FA Cup tie with a dashing display rounded off by a stunning free-kick.
There were also goals for Gareth Barry and for Portuguese midfielder Marcos Lopes on his debut, who only turned 17 last week.
Watford's best chance came with score at 1-0 when Fernando Forestieri was through one-on-one but City's goalkeeper Costel Pantilimon, in for the rested Joe Hart, pulled off an excellent diving save.
Watford boss Zola added: "Maybe it would have been different if that had gone in. I admit they deserved to win but the scoreline was a bit unfair.
"We put a lot of faith in our young players and they did so well for us."
Zola made six changes but insisted most of those were down to injury and not because he was prioritising promotion to the top flight over the FA Cup.
"I believe it was the best team I could put out," he said.
- Sports & Recreation
- Gareth Barry
- Carlos Tevez
- Fernando Forestieri
- Costel Pantilimon