The Portugal forward made it 1-1 by side-footing home Mesut Oezil's pass in the ninth minute, two minutes after Villarreal midfielder Cani had flicked the ball over goalkeeper Iker Casillas to open the scoring.
Villarreal's slick passing game troubled Madrid, and Bruno Soriano's exquisite 18th-minute pass put Ruben Castro through alone on goal to lob Casillas for a 2-1 lead.
However, Ronaldo headed in Xabi Alonso's swerving free kick inside the crowded Villarreal area just before the break to equalize.
Ronaldo scrambled to recover a loose ball in the 79th right after blowing an excellent chance in front of goal. He then swiveled before tucking a low shot past goalkeeper Diego Lopez inside the near post for a league-leading 22nd goal.
