It sealed a 7-1 aggregate triumph and a place in the Copa Sudamericana second stage.
Valencia gave Emelec the lead at the Estadio George Capwell by notching in the 42nd minute from Polo Wila's cross, and doubled their advantage by heading home a Marcos Caicedo pass five minutes after the break.
Angel Mena made it 3-0 at the 61st minute before Valencia rounded off his treble by converting Fernando Gimenez's cross nine minutes later.
Emelec's next rivals will be Chilean side Universidad Catolica, who won 1-0 against Cerro Porteno in Paraguay en route to a 2-1 overall success.
Ismael Sosa netted the game's only goal in the 57th minute, finishing off a swift counter-attacking involving Fernando Meneses and captain Cristian Alvarez.
Catolica coach Martin Lasarte was delighted by his team, telling reporters in Asuncion: "It was not easy tonight, but we scored the necessary goal. We could have netted one more, but then suffered too much.
"If we had scored once more, the tie would have been over. Our players were extraordinary. We managed to control the game."
Another Chilean team to advance was Colo Colo, who overcame Uruguayan debutants El Tanque Sisley 2-0 - 3-0 on aggregate.
Colo Colo took the lead in the 12th minute, when Fabian Benitez finished off a cross by Gonzalo Fierro. And Javier Toledo, who grabbed the winner in the first leg, made the result absolutely safe with another goal three minutes later in the heavy rain.
In Peru, Colombia's Itagui defeated hosts Juan Aurich 3-2 - 6-2 on aggregate - and will take on Uruguay's River Plate in the next round.
The 3-0 first-leg scoreline was too much for Juan Aurich to overcome and they never looked like threatening a comeback.
Itagui took a two-goal lead early in the first half through Braynner Garcia and John Restrepo. Juan Aurich equalised on the night courtesy of goals from Roberto Ovelar and Junior Viza, but Victor Cortes handed Itagui the win with four minutes to go.
Elsewhere, Paraguayan side Nacional ensured their progress on away goals by drawing 1-1 with The Strongest in La Paz.
After a goalless draw in the first leg, Silvio Torales put Nacional ahead in the fourth minute with a long-range shot. They seemed to feel the effects of playing at 3,600 metres above sea level and The Strongest levelled four minutes into the second half through Jair Reynoso, but the hosts could not engineer a winner.
Finally, in Colombia, La Equidad drew 0-0 with Venezuela's Trujillanos but went through thanks to last week's 1-0 away win.