The Republic of Ireland goalkeeper has been overtaken by Joe Hart who was between the posts in the 2-0 victory against Timisoara on Thursday night in the play-off second leg which saw City progress 3-0 on aggregate.
It was Hart's fourth successive clean sheet at the start of the campaign, but Mancini said: "The position of goalkeeper is different. I can't change every time and Shay knows this very well.
"Joe knows this too. I am sorry for him. Maybe now we are in a group, probably it is possible (he will play). But to repeat, we can change the other players, but the goalkeeper is different in my opinion."
Mancini cannot wait for Friday's draw and said: "It is an important trophy. I think the Europa League is difficult because you play more games
"But if we can change some players every game, I think we can arrive at the end and play in the final. It is not like the Champions League, sure, but it is important.
"It was vital we played a good game tonight and and now we are in the group stages."
Shaun Wright-Phillips made the breakthrough after a glorious through ball from Patrick Vieira and that settled City down.
Dedryck Boyata, 20, then had his moment to savour - a thumping header at the far post following a free-kick from David Silva.
Mancini continued: "Boyata did very well. I am happy because he scored a goal, his first goal, and that is important.
"He played often in pre-season. In the last three games he didn't play, but he is always ready. This is important because when one player is ready every time you call him to play, it is very good."
Source: PA
Source: PA