Alejandro Chumacero was on the scoresheet in the second half for the Bolivian outfit, who jumped to nine points and two clear of both Emelec and Internacional.
Chumacero's effort from the edge of the area took a massive deflection on its way past Esteban Dreer in the 58th minute.
Internacional and Universidad Chile (three points) are behind the top two in Group Four.
Santa Fe enjoyed a far more convincing win, beating Colo Colo 3-0 at the Estadio Monumental David Arellano.
Luis Paez, Omar Perez and Yerry Mina all scored for the Colombians away from home.
The opener came in the 31st minute as Paez used his smart foot skills before firing in with his left, while Perez struck early in the second half with a 30-yard screamer.
Mina headed in a 68th-minute goal to seal victory for Santa Fe, who top Group One and are level on points with Colo Colo.
Atlas remain a chance of advancing from that group after edging Atletico Mineiro 1-0.
In Peru, Juan Aurich suffered a 5-4 loss to Tigres UANL in Chiclayo.
Enrique Esqueda netted a hat-trick for the Mexicans, who were 3-2 down early in the second half before fighting back.
Tigres UANL finished unbeaten in Group Six, having already booked their place in the next round prior to Wednesday's game.
River Plate joined them in advancing after claiming a 3-0 victory at home to San Jose.
Sao Paulo sit second in Group Two after a come-from-behind 2-1 win at Danubio, with Alexandre Pato on the scoresheet.
