Villarreal took an early lead at home with two goals from Takefusa Kubo and Carlos Bacca within the first 20 minutes, but Kayode pulled one back for the visitors at the Estadio de la Ceramica.
A few minutes after Kayode’s effort, Yatabare grabbed the equaliser for Sivasspor as the teams found themselves level at the break.
After the restart, Juan Foyth restored Villarreal's lead in the 57th minute but it was short-lived as Gradel made it 3-3 seven minutes later with his maiden goal in the European competition.
The encounter turned to a dramatic finish following the introduction of Paco Alcacer for Bacca in the 70th minute.
Four minutes later, Alacacer fired Unai Emery's side ahead again and he sealed their victory with his second goal of the night in the 78th minute.
Mali goalkeeper Mamadou Samassa was in goal for Sivasspor while Kayode and Gradel were in action for 82 minutes before they were replaced by Ivory Coast's Arouna Kone and Oztekin.
On the other hand, Nigeria’s Samuel Chukwueze delivered an impressive performance for Villarreal and he was in action from start to finish.
Following the thrilling home victory, Emery's Villarreal will shift their attention to Sunday's La Liga clash against Cadiz while Sivasspor are scheduled to play Rizespor on Monday before resuming their Europa League campaign on October 29.