Having essentially wrapped up the trophy after accounting for Universidad San Martin last weekend, Roberto Mosquera's men made no mistake as they ended their season in perfect fashion.
Hernan Trigoso headed home from a free-kick to get his side off to the perfect in the 14th minute before German Pacheco sealed the win, tapping home an Oscar Vilchez cross just after the hour mark.
The fiery contest reached boiling point in the final 10 minutes with Juan Aurich's Jair Cespedes given his marching orders after receiving his second yellow card before Junior Viza and Universitario's Antonio Gonzales joined him on the sidelines three minutes later.
But it mattered little as Juan Aurich closed out the match, giving Mosquera the second major trophy of his managerial career.
The win means Juan Aurich will play-off against the winner of the Torneo Clausura, due to begin this weekend, to determine the winner of the overall championship.
Second-placed Melgar continued their disappointing end to the season, playing out a 1-1 draw against Alianza Lima to leave them winless in their last three games.
Cesar Vallejo capped off their season on a high, taking advantage of Universistario's loss to jump into third place thanks to a 2-0 win over Real Garcilaso.
Luis Tejada was the difference between the two sides with the striker scoring a goal in either half to take his Apertura goal tally to six.
Mid-table Cienciano had Gary Correa to thank for their 2-1 against Union Comercio.
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