The 30-year-old ended a scoring drought stretching back to March with two goals in the 2-2 La Liga draw at Villarreal on Sunday but was sent off in stoppage time.
Ironically it was Koulibaly whose injury-time winner had given Napoli there only victory in the Allianz Stadium under former coach Sarri in April 2018.
Man of the Match Everton added a third when he cut in from the left and unleashed a low shot that sneaked inside Gallese’s near post and Dani Alves made it 4-0 eight minutes into the second half.