The sides went into the second leg level after a 1-1 draw in Pereira but Gimenez - on target in Emelec's 5-0 Primera A win over El Nacional at the weekend - continued his streak to open the scoring on Tuesday.
Gimenez needed just four minutes to break the deadlock and boost his side's hopes of progression before the Colombian outfit levelled after an hour.
As both sides went in search of a winner, Gimenez left it late to send Emelec through and set up a meeting with either Chile's Universidad Catolica or River Plate in the next round.
Universidad Catolica of Ecuador needed penalties to ensure their victory over Deportivo Anzoategui.
Having drawn the first leg 1-1, Rolando Escobar edged the hosts in front early in the second leg before Armando Wila scored from the spot with three minutes remaining.
That took the game to penalties as the visitors held their nerve to move into the second round.
The goals continued to flow between San Jose and Huachipato as the Chilean Primera Division outfit came through 6-3 winners on aggregate.
Early goals from Lucas Simon and Carlos Espinoza took Huachipato's aggregate lead to 5-1 before Cristian Diaz pulled a goal back.
Leonardo Povea restored the four-goal cushion and, while Diaz managed to score a second, the visitors moved into the next round where they will take on Catolica.
Deportes Iquique and Rentistas both bowed out despite picking up narrow second-leg wins.
Iquique were unable to turn around a deficit from the first leg against Club Universitario, winning 1-0 but losing 2-1 on aggregate, while Javier Alles' goal was not enough to see Rentistas through against Cerro Porteno, who also claimed a 2-1 aggregate triumph.
