Barcelona's goalkeeper Wojciech Szczęsny tries to save a shot, during a Champions League opening phase soccer match between SL Benfica and FC Barcelona at the Luz stadium in Lisbon. AP
The Catalan giants brought former Polish international Szczesny out of retirement as an emergency signing in October after Marc-Andre ter Stegen suffered a severe knee injury.
Pena has been the club's number one during the first half of the season but Szczesny was chosen in the previous two matches.
"My job is to make the decision on this position... for me Tek (Szczesny) is an experienced player and he has a good personality, but both of them are great goalkeepers," Flick told a news conference ahead of the Champions League clash with Atalanta on Wednesday.
"I decided, also with my team, my coaching staff, for Tek... both are very good, and in the past Inaki did a good job, but now I decided like that.
"I always look for the (good of) the team, and this is how we act."
Barcelona already secured qualification directly to the last 16 of the Champions League with a 5-4 win over Benfica last week, in which Szczesny made two big mistakes which led to goals.
However Barcelona have won each of the five matches in which the former Juventus stopper has featured this season.
Barcelona will be without defender Andreas Christensen, who will miss three weeks with a calf injury, the club said in a statement.
The Danish defender had only just recovered from an Achilles tendon issue and has not played since August.
Atalanta, third in Serie A, are hoping to secure a top eight Champions League finish, with the Italian side currently seventh.
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