The Group A leaders barely salvaged a draw in their first match of the championship phase, but were humbled on the road at Casagrande - and finished the match with 10 men.
Daniel Chavez and German Alemanno struck for Cesar Vallejo during the second half, before Luis Guadalupe was handed a straight red card in the second minute of added time as Garcilaso's hold on top spot began to weaken.
Sporting Cristal consolidated second spot in the group, winning 1-0 away at Pacifico to close the gap on Garcilaso to three points.
Cristal's Joazhino Arroe scored the winner on 11 minutes.
Alianza Lima (third), Cesar Vallejo (fourth) and Sport Huancayo (fifth) all won as the pressure to get to the top increased.
Lima had a 3-0 triumph at home to Union Comercio, with Wilmer Aguirre netting a brace.
Huancayo had Ryan Salazar's eighth-minute strike against Melgar to thank for a 1-0 result.
In Group B, Universitario and Inti Gas both won, with the former remaining eight points clear top of the division.
Manuel Ruidiaz scored a brace to help Universitario battle back from an early deficit to defeat UTC Cajamarca on the road 2-1.
Inti Gas handled the threat of 10-man Leon de Huanuco 2-0, although it took them until the 90th minute to score the second and secure the three points.
A Josias Cardoso double helped Cienciano get past Jose Galves 2-1, although not after some nervous moments late.
Jersson Vasquez's goal with eight minutes to play came just before the dismissal of Cienciano's Enzo Scorza in the 88th minute, but the home side held on one man down.
Rodrigo Cuba fired Juan Aurich to a 1-0 victory over Universidad San Martin.
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