First-half goals from Gareth Bale and Cristiano Ronaldo saw Real Madrid lead at the interval, but Villarreal scored twice in the second period through Roger Martinez and Samu Castillejo as the points were shared on the night.
The draw means that Atletico Madrid are confirmed as second-placed finishers in Spain's top flight this season, with Real Madrid in third and Villarreal ending the campaign in fifth.
Read how it all unfolded in Sports Mole's minute-by-minute live commentary of the action below.
VILLAREAL: Andres; Mario, Bonera, Alvaro, Marin; Soriano, Rodrigo, Fornals, Fuego, Sansone; Unal
REAL MADRID: Luca Zidane; Carvajal, Ramos, Varane, Marcelo; Casemiro, Modric, Kroos; Ronaldo, Bale, Isco
Celta 4-2 Levante, Leganes 3-2 Betis, Las Palmas 1-2 Girona, Malaga 0-1 Getafe, Sevilla 1-0 Alaves