Going into the match with an unassailable four-point lead over Universitario, Freddy Garcia's men secured the victory through Fabio Ramos' 57th minute spot kick.
Garcilaso will now head into the second phase of their domestic campaign as the number one seed.
Universitario held on to second position as they thumped nine-man Jose Galvez 5-1 at home.
Raul Ruidiaz scored an extraordinary four goals, with his first-half brace coming within the first 28 minutes.
The deadly striker completed his hat-trick on 56 minutes before adding a fourth in the 74th minute.
A fifth was added by Universitario's Jankarlo Chirinos in stoppage time.
Jose Galvez's sole goal came through Junior Alberti's 35th-minute penalty and they had two players, Fisher Guevara and Ricardo Salcedo, sent off in the second half.
Sporting Cristal came from a goal down to defeat Cesar Vallejo 4-2, with Carlos Lobaton's two late strikes proving the difference.
Vallejo led the contest for five minutes when Daniel Chavez put them 2-1 up on 32 minutes.
But Horacio Calcaterra's leveller saw the contest level until the 87th minute when Lobaton snatched the lead back for Cristal.
Lobaton scored Cristal's fourth from the penalty spot in stoppage time.
In other results, UTC Cajamarca overcame Juan Aurich 2-1, Leon de Huanuco won 1-0 against Union Comercio and there was a goalless draw between Pacifico and Cienciano.
Inti Gas stunned Alianza Lima 3-1 and Melgar defeated Sport Huancayo by a 2-0 scoreline.
