In Santiago de Chile, a week ago, the two teams tied without goals.
The Colorado team, in which Argentine creative Andrés D'Alessandro stands out, began to build their victory with Boschilia's goal, who came on in the 14th minute replacing the injured Patrick.
Boschilia scored just before half-time after stealing the ball from Carrasco in a goal kick.
Marcos Guilherme, who had replaced D'Alessandro, sealed the match with an individual play in the 76th minute.
In the third round, the last one before accessing the group stage, Internacional will face the winner of the tie between Ecuador's Macará and Colombia's Deportes Tolima.
Internacional came out in search of an early goal. Coudet entrusted the attack to Peruvian Guerrero and Argentine D'Alessandro, two experienced players who showed great level today.
Coudet had to make an early change due to Patrick's muscular injury before the first quarter of an hour was completed.
On the part of the Universidad de Chile, containment and patience. Hernán Caputto's players barely approached the Colorado's area and buried their chances in a Diego Carrasco's mistake.
The Chilean center-back did not control a pass from his goalkeeper well and Boschilia, Patrick's substitute, stole the ball from him, headed towards the area and scored his first goal with the Inter's shirt.
The Universidad de Chile took a step forward with Charles Aránguiz and Jean Beausejour on the left and put their rival in certain difficulties. A goal would classify them and the Beira-Rio's stands started to get nervous.
But a counterattack led and finished by Marcos Guilherme ended all hope for the visitors and gave tranquility to an Internacional decided to go to the group stage.