But three goals in the opening 10 minutes of the second period guided Atletico's second-string team to a 4-0 victory at Wanda Metropolitano Stadium on Wednesday.
Thomas Lemar scored for Atletico in the 48th minute, Nikola Kalinic in the 53rd, Angel Correa in the 55th and Victor "Vitolo" Machin in the 81st to secure Diego
Simeone's team a place in the last 16 following a 5-0 aggregate victory.
"We struggled in the first half. We weren't able to play with quick transitions," said Simeone after his 400th Atletico match.
"Everything changed in the second half. After the first goal the team played more freely."
Atletico was without Diego Costa because of injury, while Antoine Griezmann and several other regular starters were rested by Simeone, who was banned from the bench as he served the second of a three-game suspension following a rant in a Copa match against Sevilla last season.
Substitute Lemar went on at halftime and was key for Atletico, opening the scoring with a right-footed shot from outside the area. Kalinic added a header and Correa produced a fine finish with the outside of his right foot. Vitolo's goal from close range came after a pass by Saul Niguez.
Barcelona midfielder Ricard "Riqui" Puig, 19, set up one of Suarez's goals on his debut.
"It was a dream come true," Puig said. "I used to come to this stadium when I was three."
Malcom went off in the final minutes with an apparent knee injury.
Toko-Ekambi became the first Villarreal player to score four goals in a match this century, leading the club to an 11-3 aggregate win. He netted three times in the first half and once in the second.
In all first-division ties, Girona came from behind to defeat Alaves 2-1 and advance 4-3 on aggregate, while Real Sociedad beat Celta Vigo 2-0 to go through 3-1 overall.
Alaves struck first at Montilivi Stadium in Catalonia with an own-goal by Pedro Alcala in the 62nd minute, but the hosts rallied through Alex Granell in the 74th and Cristian "Portu" Portugues in the 79th to reach the last 16 for the first time.
Sociedad sunk Celta with two superb goals by Mikel Oyarzabal and Adnan Januzaj. Oyarzabal netted in the 10th with a booming long-range shot into the top corner, and Januzaj scored in the 27th with a curling strike.
Sevilla edged third division Villanovense 1-0 to advance following a 0-0 first-leg draw. Andre Silva scored the winner early in the second half, converting the rebound after missing a penalty.
Valladolid came from behind to defeat second tier Mallorca 2-1 and progress 4-2 on aggregate.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)