On the half-hour mark, it was Cesena who took the lead as Guido Marilungo headed in from close range after his initial effort had come back off the bar.
They scored a second just two minutes later when Gregoire Defrel found himself some space outside the box, before driving an effort into the bottom corner.
Rugani almost pulled a goal back for Empoli on the stroke of half time, but, after latching onto Manuel Pucciarelli's pass, he fired a strike wide of the post.
Empoli then had a chance to level the scores, but Verdi saw his effort from inside the box saved by the keeper.
However, they did manage to equalise in the 72nd minute through Rugani, who poked in from close range after the hosts had failed to clear a corner.
In stoppage time, Marilungo almost snatched the three points for Cesena, but his header was saved at point-blank range by Luigi Sepe as the game finished level.