Former Watford striker Marvin Sordell put the Trotters in front with a penalty at Vicarage Road but Vydra scored his 11th in six games to level it up and then turned supplier for Almen Abdi for the winner.
Zola's men were upset at lowly Bristol City in midweek but Vydra's performance ensured they banished the memory quickly.
Zola said: "Matej 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 today. 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."
"Their 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."
"I think today 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."