In their last fixture before facing Liverpool in the Champions League final in Kiev, Zinedine Zidane’s side had taken a 2-0 first-half lead through Gareth Bale and Cristiano Ronaldo.
The latter was involved for his club for the first time since sustaining an ankle injury during the clash with FC Barcelona earlier this month, playing 62 minutes.
Villarreal launched a comeback after the interval, however, and goals from Roger Martinez and Samu Castillejo meant the European Cup holders had to settle for a point that confirmed a third-place finish in La Liga.