Caracas needed a miracle to go through after losing the first-leg 4-0 in Montevideo but never looked like troubling Fabian Carini in the opening stages of the game.
Fabian Estoyanoff put Peñarol ahead on 27 minutes, meaning Los Rojos de Avila needed to score six to advance due to the away goal rule.
They eventually found a goal thanks to Edwin Paraza's headed effort with twelve minutes left on the clock, but that was too late.
The referee Sandro Meira almost suspended the encounter towards the end due to the many lasers coming from the supporters in the stands.
The game finished eventually 1-1 with los Carboneros progressing 5-1 on aggregate.
Peñarol will be in Group 8 along with Godoy Cruz of Argentina, Universidad de Chile of Chile and Atletico Nacional of Colombia.