Earlier, Barca had momentarily usurped Real thanks to Lionel Messi’s winner four minutes from time in a 2-1 victory at Atletico Madrid.
Real lead Barca by a point, but also have a game in hand on their title rivals.
“We showed character to turn the game around,” said Real boss Zinedine Zidane.
“With everything that happened today it was vitally important to get the three points.”
Bale was recalled to the starting line-up for the first time in three months after a long-term injury layoff and Real’s shock 2-1 defeat to Valencia in midweek.
And the European champions looked set for a second straight defeat as Villarreal struck twice early in the second half.
Firstly, Manu Trigueros volleyed home Samu Castillejo’s knockdown before Cedric Bakambu burst onto Bruno Soriano’s through ball to slot past Keylor Navas.
Ronaldo almost replied immediately, but Madrid’s luck looked out when his sweetly struck volley came back off the post.
However, Bale started Madrid’s fightback as he rose highest to power home Dani Carvajal’s cross 25 minutes from time.
Villarreal had enjoyed the better of the opening hour, but were swamped by wave upon wave of Real attack for the final 30 minutes.
The visitors needed a slice of luck, though, when Soriano was harshly adjudged to have handled inside his own area 15 minutes from time.
Ronaldo took responsiblity from the spot to smash home the equaliser.
Villarreal had lost goalkeeper Sergio Asenjo midway through the first half to what looks like the fourth cruciate knee ligament injury of his career.
“Asenjo seems to have torn his ACL (anterior cruciate ligament) in his left knee. It’s a real shame,” said Villarreal coach Fran Escriba.
And his absence was to prove crucial for Real’s winner seven minutes from time as substitute goalkeeper Andres Fernandez let Alvaro Morata’s powerful header from Marcelo’s cross squeeze under his body to complete a rousing Real fightback.
– Messi to rescue –
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Under-fire Barcelona coach Luis Enrique thanked the “terrible” state of Atletico’s pitch for Messi’s winner at the Vicente Calderon.
PTI