Emery's side defeated Villarreal 2-1 at home to wrap up a 5-2 aggregate victory in the Europa League round of 16 but had to do so without Banega, who missed the match after reporting some discomfort in his quad at training on Thursday.
Emery picked Vicente Iborra to replace Banega in Sevilla's attacking midfield slot but conceded his team had not dealt with the Argentine's absence very well to begin with at the Estadio Ramon Sanchez Pizjuan.
Banega had played in seven of Sevilla's previous nine Europa League games.
"We lacked a bit of control and the late absence of Banega had an impact on us," Emery told Gol TV. "But we focused on where we were strong and we waited for our chances to come."
After a scratchy start at home, Sevilla opened the scoring through Iborra in the 69th minute and although Giovani dos Santos equalised for Villarreal, Denis Suarez's header with seven minutes remaining saw Emery's team triumph.
Sevilla's coach insisted he has no preference as to who they face next in the Europa League, which they won last season.
The La Liga club were joined by Wolfsburg, Fiorentina, Dynamo Kiev, Napoli, Club Brugge, Dnipro Dnipropetrovsk and Zenit in reaching the quarter-finals on Thursday.
"We do not want any rivals in particular. The hype will end up taking over," Emery said.
"We'll wait to find out who we draw and then we'll prepare."
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