Johan Fano gave Huanuco the lead in the 41st minute and they held the advantage through until the half-time break.
But it did not take Universitario long to wrestle back the advantage with Christoper Gonzales equalising on 60 minutes before Manuel Ruidiaz snatched the lead with the winning goal three minutes later.
Universitario now lead Group B by 12 points with three games to play after UTC Cajamarca's 4-0 loss to Universidad San Martin - with the group winner advancing to play the Group A winner in the final.
It is a much tighter scenario in Group A with Sporting Cristal's 5-2 win over Real Garcilaso earning them group leadership - displacing their defeated opponents.
Sporting striker Irven Avila scored a hat-trick as Real Garcilaso was on the back foot after Marcio Valverde's ninth minute spot-kick.
Third-placed Alianza Lima conceded a late equaliser as they drew 1-1 at Melgar.
Sporting Cristal (69 points) leads Group A from Real Garcilaso (68) and Alianza Lima (65).
In other Group A matches, Cesar Vallejo eclipsed Sport Huancayo 3-2 while Union Comercio thrashed Pacifico 4-1.
In Group B, Cienciano won 2-1 against Juan Aurich and Jose Galvez accounted for Inti Gas by a 4-0 scoreline.
