Udinese loanee Almen Abdi and Nathaniel Chalobah had the hosts cruising at 2-0 in the opening 15 minutes, only for Peter Ramage and veteran Kevin Phillips to strike.
A victory would have taken either side into second spot in the Championship, but Watford had to settle for climbing up to third, level with Leicester.
"After the first half we were not expecting anything like that," Zola said.
"They played really well and caused us a lot of problems and we did not have the same freshness in our legs. And Phillips certainly made a difference.
"But there are 15 games to go and I don't want to be second now, I want to be second at the end of the season. It's going to be a race to the end."