A Johnny Vegas own goal and strikes from Fabio Ramos and Alfredo Ramua saw Freddy Garcia's men to the comfortable victory at the Estadio Municipal de Urcos.
They finished top of Group A – two points clear of Sporting Cristal – and will face Universitario in a two-legged play-off.
Ramos set up the opener on three minutes as his cross from the left was bundled in clumsily by Pacifico goalkeeper Vegas.
He then curled a free-kick over the bar, before doubling his side's advantage on 31 minutes.
A ball was played into Ramos' path and the captain drilled a powerful left-footed effort past Vegas from 18 yards.
Ramos was at the centre of everything throughout and he set up the sealer with 13 minutes remaining.
He played a square pass for Ramua, who took a few touches before beating Vegas from outside the area.
The duo celebrated the sealing goal with a dance as Real Garcilaso secured a spot in the play-off, which begins on December 8.
Pacifico's loss was particularly costly as they slipped into the relegation place after Union Comercio claimed a 2-0 win at home to Sport Huancayo.
It meant Sporting Cristal's 4-1 thrashing of Melgar mattered little as they finished second in Group A.
Elsewhere in the group, Alianza Lima drew 1-1 at home to Cesar Vallejo.
In Group B, Universitario warmed up for the play-off with a 2-2 draw at already relegated Jose Galvez.
UTC Cajamarca were 4-2 winners at Inti Gas, Juan Aurich claimed a 1-0 victory at Leon de Huanuco and Cienciano edged Universidad San Martin 1-0.
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