Nibali, winner on Thursday's stage four, came home seventh on the 174km trek from Acqui Terme to Frabosa Soprana.
Colombian Betancur (Acqua & Sapone) pipped David Rebellin (Meridiana) by a second following a challenging climb to the summit finish.
Matthew Rabottini took third for Farnese Vini - three seconds off the winner's pace - on the stage while the final podium is filled by 30-year-old Sicilian Nibali and fellow Italians Riccardo Chiarini and Franco Pellizotti, who both ride for Androni Giocattoli.
Nibali was third overall on this year's Tour de France behind Britons Bradley Wiggins and Chris Froome.
It is the second running of the race. The first in 2011 was won by Ivan Basso.