Botafogo won Wednesday's second leg in Rio de Janeiro 4-0 to overturn their 1-0 defeat in Ecuador last week, with Wallyson scoring the first three goals for the home side.
The visitors entered the Maracana with a slight advantage thanks to Victor Estupinan's goal in Quito but with a strong crowd cheering on the hosts, Botafogo were the favourites to progress.
The Brazilian side dominated possession throughout the match but had to wait until the 37th minute to notch their first goal, with Wallyson volleying home from Jorge Wagner's flicked header.
Nicolas Lodeiro teed up Botafogo's second goal with the Uruguayan midfielder releasing Wallyson into the left channel in the 67th minute and the 25-year-old Brazilian striker burst forward before cutting inside a defender to score.
Wallyson completed his hat-trick with 10 minutes remaining, again getting in behind Quito's defence on a fast break and picking up Elias' pass before finishing past visiting goalkeeper Rolando Ramirez.
Henrique wrapped up Botafogo's win with a scrappy goal in second-half injury time.
In the 19th minute, both sides lost a player after Zezinho of Atletico PR and Cristal's Adan Balbin clashed.
Cristal had arrived in Brazil with a 2-1 lead after victory in the first leg and, while the hosts levelled the tie just after the hour-mark through Manoel, Irven Avila's goal just a minute later put the Peruvian visitors back in front.
But in the 96th minute, Marco Ortiz conceded a penalty and was sent off and Atletico PR's Ederson converted from the spot to force a shootout.
Cristal slotted their first three penalties to lead 3-2 and when Nathan missed Atletico PR's fourth spot-kick, the home side again looked in an untenable situation.
