The Catalans humbled Atletico in the first leg last Tuesday thanks to a superb hat-trick from Lionel Messi and the Argentine forward was on target again on Sunday, hitting the winner in the 3-2 Primera Liga win at Osasuna.
The Atletico players have rallied round Aguirre. Goalkeeper Leo Franco said criticism from fans after Sunday's 3-2 woeful home loss to Athletic Bilbao was unfair while defender Antonio Lopez called for patience.
"The players are the ones who are to blame because he (Aguirre) is not out there on the pitch," Franco said on the club's website.
"We need to try to get back on the winning trail and then I am sure the cat calls directed at the coach will stop."
Atletico's task of stopping Messi and Barca's other prolific forwards, including the league's top scorer Samuel Eto'o and Thierry Henry, will be complicated by the absence of central defender John Heitinga.
The Dutchman is suspended for one match after he was sent off in the first leg for felling Messi in the penalty area, but Franco said he and his team mates still believed they had a chance of making it through to the quarter-finals.
"We are not going there for a stroll," he said. "We are confident of our chances and I sincerely believe we can do it."
In other Cup second legs on Wednesday, Sevilla travel to Deportivo Coruna with a 2-1 lead from the first leg having also beaten the Galicians 3-1 in the league at the weekend.
Holders Valencia host Racing Santander level at 1-1 and Real Valladolid need to reverse a 3-1 loss at Sporting Gijon in the first leg having also lost to them 2-1 in Sunday's league game.
Struggling Real Mallorca, thumped 3-0 by Real Madrid on Sunday, will be defending a 3-1 advantage at Almeria.
There are two non-Primera Liga teams left in the competition, Segunda B (third tier) sides Poli Ejido and Real Union, conquerors of Real Madrid in the previous round.
Poli Ejido travel to Barcelona looking to defend a 3-2 advantage over Espanyol while Real Union play Real Betis in Seville trailing 1-0.
In Thursday's one remaining match, Osasuna, currently bottom of the league, and Athletic Bilbao are tied at 1-1 following the first leg in Pamplona.
Thank you for reading 5 articles this month* Join now for unlimited access
Enjoy your first month for just £1 / $1 / €1
*Read 5 free articles per month without a subscription
Join now for unlimited access
Try first month for just £1 / $1 / €1