The Frenchman nudged in from close range in the 26th minute to give Eduardo Berizzo's side the lead after a storming solo run from Argentine Joaquin Correa, who coasted past four players before cutting the ball back for his team mate to score.
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Ben Yedder then latched onto a simple through ball from Franco Vazquez after some smart passing in midfield to tuck the ball under visiting goalkeeper Jasmin Handanovic and in off the far post in the 37th.
He completed his hat-trick with seven minutes remaining from the penalty spot, slamming the ball just under Handanovic and into the bottom corner after his compatriot Sebastian Corchia was knocked over in the area.
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Sevilla, who battled back from 2-1 down to draw 2-2 at Liverpool in their first game, top the group with four points from two matches after Juergen Klopp's side drew 1-1 at Spartak Moscow.
Five-times Europa League winners Sevilla went into the game on the back of a 2-0 loss at Atletico Madrid, which halted a run of four straight domestic victories, but quickly put it behind them.
They swiftly got on top with Ben Yedder and Steven Nzonzi each testing Handanovic inside seven minutes.
The Slovenian champions managed to carve out a couple of early openings through Brazilian striker Marcos Tavares but were sliced open themselves by Correa, allowing Ben Yedder to break the deadlock.
It was all too easy for the Los Nervionenses from then on, with Nolito spurning several chances to join Ben Yedder on the scoresheet while Jesus Navas hit the post moments before the Frenchman completed his treble.
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