Pouring rain made conditions difficult at the Benito Villamarin, and that slippery surface led to Villarreal’s Gerard Moreno losing his footing when his shot from inside the area was blocked.
Giovani Lo Celso then wasted another glorious chance for the visitors, as Rui Silva dashed off his line and made a superb stop, before Moreno failed to hit the target from close range.
Betis were struggling to get into the game, but they did see a Rodri shot saved, while Youssouf Sabaly blazed harmlessly off target from distance.
The hosts should have been behind at the break though, as Nicolas Jackson missed two huge chances and Moreno had a thumping drive from the edge of the area well saved.
Manuel Pellegrini must have given his side a stern talking to at the break, as they were dominant in the second half.
Borja Iglesias spurned one chance, hammering just past the post from inside the area, but they took the lead with their next shot when Rodri steered home a stunning, fierce right-wing cross from Luiz Henrique.
That was the first league goal Villarreal had conceded this season, and a second nearly followed moments later when Henrique saw a shot of his own saved.
At the other end, substitute Francis Coquelin dragged an effort just wide from 20 yards, but the visitors lacked the cutting edge they had earlier enjoyed, allowing Betis to win for only the second time in seven H2H meetings.
Flashscore Man of the Match: Luiz Henrique (Real Betis)
