The away win by the club that started the day second to last against the only team below them extended Empoli's unbeaten run to four games since Nicola took over on January 15.
Empoli rose four places to 15th. They are eight points clear of Salernitana.
Visitors Empoli were fortunate to take the lead midway through the first half.
Nicolò Cambiaghi's cross from the left took a deflection off the head of defender Alessandro Zanoli and looped over his stranded goalkeeper.
M'Baye Niang secured the win from the penalty spot three minutes from the final whistle and Matteo Cancellieri completed the scoring with a fine breakaway finish in injury time.
Inter Milan top the league and are four points clear of Juventus with a game in hand.