Colombian attacker Muriel put the hosts ahead before captain Papu Gomez scored with a superb second-half strike to secure a vital win that keeps their hopes alive heading into the final Group C round of fixtures.
The Italian minnows who are hosting their home European fixtures at the San Siro while regular stadium in Bergamo undergoes renovations travel to second-placed Shakhtar Donetsk in their final game.
The Italians sit fourth in Group C and must secure a win and hope that leaders Manchester City beat third-placed Dinamo to secure qualification to the last 16.