The Swiss side came from two goals behind against 10 men to stay three points clear at the summit of Group I, with Federico Bernardeschi putting the Italians into a two-goal lead.
A late Mohamed El-Nenny strike helped Basel come from two down to draw 2-2 at home to Fiorentina on Thursday, securing passage to the next round of the Europa League as the Group I winner.
A couple of composed Federico Bernardeschi finishes either side of a red card for Facundo Roncaglia put the Serie A side in control, but the hosts ultimately made their numerical advantage tell.