The 25-year-old, who netted for the Black Stars in a 3-1 win over Mauritania in an international friendly on Tuesday, curled a sweet ball into the top right corner to help Los Rojiblancos claim all three points away at Estadio de Mendizorroza.
He has now tallied three league goals in 25 matches involving 16 starts.
Atletico opened the scoring in the fifth minute through Saul Niguez whose shot slipped through the legs of goalkeeper Fernando Pacheco into the net.
Six minutes later, Diego Costa made it 2-0 for Los Rojiblancos, curling a sweet shot into the net from outside the box after receiving a pass from Koke.
In the 59th minute, Alvaro Morata, having been played through by Thomas Lemar on the run of play, dashed into the Alaves box before sending the ball past the goalkeeper to make it 3-0.
Then Partey struck six minutes to full-time, delivering a curling shot from about 25 yards into the top left corner of the net.
Diego Simeone's outfit sit second on the league table, three places above Abelardo Fernandez's side.
Saturday's game featured more than one Ghanaian.
Black Stars ace Mubarak Wakaso came on for Alaves in the 68th minute, five minutes before compatriot and club-mate Patrick Twumasi was thrown into the game.