Bale has endured a difficult time at Madrid due to a strained relationship with head coach Zidane, fan criticism and a failed move to Chinese Super League side Jiangsu Suning.
But after staying, Bale has started the season well and scored for the first time since March on Sunday, netting both goals as Madrid battled to a stalemate in LaLiga action at Estadio de la Ceramica.
Bale's second goal came four minutes from time and ensured Los Blancos earned a point, but he was booked twice in stoppage time to be send off, putting a dampener on proceedings.
Zidane, however, was not focusing on the sour end to Bale's outing away from home.
"They were two fouls and two yellow cards," Zidane told reporters. "But now to think about a rest. Well, maybe not a rest as he's going with his national team.
"I am happy for his goals and we keep going with the positive things."
Madrid captain Sergio Ramos made an error for Villarreal's first goal, finding himself robbed of possession by Gerard Moreno in the build-up.
And while Zidane acknowledged Madrid could have been better, he remained upbeat and positive about future improvement.
When asked if there was a lack of defensive intensity, he said: "At the start of the game, yes, and in the game it's always important to start strong.
"But I think that the 30 minutes after that, we were better in everything. We got the equaliser before the break and that was important.
"We controlled the game, these things [conceding goals through errors] happen. We have to work on this, to improve our defensive ways and later offensively we know that we will create things. I will stick with the positive, the reaction. It's important we didn't lose."