Spain's all-time leading scorer bagged a brace as NYCFC ended Orlando City's unbeaten streak at home with a 3-0 victory on Sunday.
Since moving into its new stadium at the start of the season, Orlando had gone six matches without defeat at the 25,500-seat arena.
But NYCFC conquered the Orlando fortress and beat its Eastern Conference foe for the first time in seven meetings thanks to Villa, who opened the scoring in the 14th minute.
The referee pointed to the penalty spot when Orlando captain Kaka handled the ball inside the area, and Villa converted.
It got better for Orlando 21 minutes later as Rodney Wallace slid in and tucked the ball away at the back post.
Orlando had the chance to reduce the deficit just past the hour mark, but leading scorer Cyle Larin cannoned his penalty into the post.
And Villa made sure of the win eight minutes from time — rounding the goalkeeper for his eighth goal of the season — ending NYCFC's two-game winless run.
Elsewhere, Giovani dos Santos was on target as the in-form Galaxy overcame Minnesota United 2-1.
The score was level after Christian Ramirez canceled out Dos Santos' 38th-minute opener, but Ramirez deflected the ball into his own net with six minutes remaining to gift the Galaxy three points.
The Galaxy have now won back-to-back games, while they are unbeaten in four matches.