The Czech international, who attracted plenty of interest in the transfer window, scored his 19th goal of the season four minutes after Bolton had taken the lead through a penalty from Watford old boy Marvin Sordell.
Vydra then turned supplier after the break, setting up Almen Abdi for what turned out to be the winner, moving his side back within a point of second place in the npower Championship.
Zola: "He shows also why so many teams were interested in him as well. It's another performance of quality, quantity and character.
"He's been absolutely outstanding. I would say (Cristian) Battocchio as well was outstanding and a few other players.
"It was a game in which we needed to work hard because they were good and considering also it was the third game in a week, which has always been very difficult for us. I was really pleased and proud of the performance."
The Hornets' head coach said "it was essential" his side responded so quickly to going behind and added: "The penalty was a little bit 50-50 but that penalty served a purpose because after that we came back strongly, we played much better and so we reacted really well to that."
He later said: "I think the passing wasn't as good as normal. We couldn't find rhythm, it was always breaking up all the time so we couldn't get the control of the game we normally have.
"A lot of it was down to them because they were organised, aggressive and when they got the ball back they didn't lose it easily.
"That was one thing but when there are games like this you need to step up the other part of the game which is the work rate, the determination and the courage - something that I think we had, otherwise we wouldn't have won the game."