The final went to a third match after each team had won one of the two legs, "La U" 3-0 at home in Lima on Sunday after losing the first 3-2 in Cusco the previous weekend. The aggregate score is not taken into account.
"These kids really play good football, what they do is sensational, they're the future of Peruvian football," Universitario's Argentine coach Angel Comizzo said in praise of his young team.
Universitario twice had to overcome the extra obstacle of playing two of the matches in the rarefied air of Andean venues more than 3,000 metres above sea level, away to Garcilaso in Cusco and the playoff in Huancayo.
Garcilaso, a team founded in 2009 and used the playing all their home matches at 3,500 metres in Cusco, were runners-up for the second successive year.