After losing to league leaders Juventus last weekend, the White and Blacks fell to another defeat at the Stadio San Paolo despite the Ivorian scoring.
Davide Nicola’s men started the game on a poor note after the Parthenopeans raised to an early lead through goals from Amin Younes and Jose Callejon.
Kevin Lasagna reduced the deficit at the half-hour mark before the 23-year-old midfielder levelled proceedings in the 36th minute.
Second-half strikes from Arek Milik and Dries Mertens denied the Dacia Arena outfit a share of spoils and saw them drop to the 16th spot.
Fofana featured for the entire duration along with Nigeria international William Troost-Ekong who made his 27th league appearance in the encounter.