The midfielder's 40th minute opener proved crucial as it helped El Glorioso to three points in the matchday 38 fixture at Estadio de Mendizorroza.
The goal was his first and only goal of a season in which he made 29 league appearances involving 18 starts.
And it was such a beautiful goal as Wakaso hit a sweet right-footed half volley from the edge of the box after a Girona headed out a cross.
It was not until the 83rd minute before the hosts added a second when Manu Garcia received Patrick Twumasi's cross with a one-time assist for Jonathan Calleri to fire a shot into the net.
Three minutes later, Girona pulled a goal back through Cristian Portu who hit a shot into the net after being played through on goal by Pere Pons.
Alaves ultimately finished 10th on the league table while Girona ended up in the relegation zone.