Wanderers bounced back from consecutive defeats with a victory through goals either side of half-time and a game-sealing third from Diogo Jota with 15 minutes to go.
Raul Jimenez scored the first from the penalty spot in first-half injury time following a clumsy Lucas Digne foul on Daniel Podence.
Leander Dendoncker headed in the second just a minute after the restart before Jota lashed in from just inside the box to put the game beyond the visitors.
Everton committed so much of their efforts to keeping the home side at bay and as a result offered little at the other end of the pitch, with Dominic Calvert-Lewin and Richarlison given scraps to feed off at best.
The closest they came to a goal was a Digne angled drive that flashed past the far post in the second half.