The Romanian shot-stopper has featured in all of City's matches in the competition this season, but was unclear as to whether he or first-choice keeper Joe Hart would be given the nod against Wigan Athletic at Wembley.
However, Mancini has confirmed that it is only fair for Pantilimon to feature in the final.
When asked if he would select the England international, the City manager said: "I don't think so. We decided this at the start of the season. Pantilimon deserves to play.
"Joe won the FA Cup two years ago, he won the Premier League last year, he is the best keeper in England and I think he should be happy his second keeper can play in a big game.
"I know he wants to play but we decided at the start of the season it was important for Pantilimon to play in the two cups."
Pantilimon initially joined City on loan from Politehnica Timisoara in 2011.