Penarol are out of the Copa Libertadores despite a 3-0 win over Deportes Iquique on Tuesday as Emelec progressed with a draw.
Uruguayan outfit Penarol needed a win in their final Group 4 match, but a point was enough for Emelec, who finished second to Velez Sarsfield.
Marcelo Zalayeta put Penarol ahead in the 39th minute, fortuitously deflecting in Sebastian Gallegos' 30-yard free-kick and leaving Rodrigo Naranjo with no chance.
Zalayeta doubled their lead in the 74th minute, tapping in a Carlos Nunez cross after a fine attacking move.
Penarol added a third through Matias Aguirregaray, who was on hand to tap in a rebound and complete the scoring.
But the result mattered little as Emelec secured the point they needed at Velez Sarsfield, drawing 0-0 in Buenos Aires.
Santa Fe booked their spot in the knockout stages with a 2-1 win over Deportes Tolima in Group 6.
A brace from Cristian Borja led the Colombians to the victory in Ibague after Diego Chara put Deportes Tolima ahead early in the second half.
Santa Fe are guaranteed to finish in the top two, but whether they end up first or second is yet to be decided.
Tigre kept their chances of reaching the knockout stages alive with a 3-1 win at home to Sporting Cristal.
The Argentine outfit struck through Leandro Leguizamon, Matias Perez Garcia and Ruben Botta, with Carlos Lobaton's 71st-minute effort proving mere consolation.
Tigre jump up to third in Group 2 with the victory, two points behind Libertad and level on points with second-placed Palmeiras.