The Barclays Premier League leaders were eliminated from one of the four trophies they are pursuing as they went down 3-2 to their rivals in a pulsating third-round tie at the Etihad Stadium on Sunday.
The result may have been a blow to ambitious City but Roberto Mancini's men at least finished the game in the ascendancy, and with pride intact, after battling back from 3-0 down with 10 men.
City were aggrieved when captain Vincent Kompany was sent off after just 12 minutes but the ultimate manner of the defeat leaves them looking back positively.
Pantilimon, who featured as in-form first-choice Joe Hart was rested, said: "We are happy - we agreed with the fans - because the referee made it like this by expelling a player really early. I don't think that was great.
"It has not damaged our confidence. It was an interesting game, but losing a player after 10 minutes is not normal. It was a foul but a normal foul and not a direct red card.
"But in the second half we played on the counter-attack and scored two goals, but couldn't get the third goal, though we had chances."
City, who have a three-point lead at the top of the Premier League, will now turn their attention to the Carling Cup with the first leg of their semi-final against Liverpool on Wednesday.
As it stands, they will have to make do without Kompany, who is due to serve a four-match ban for what was his second red card of the season.
City have appealed against the dismissal and will find out on Tuesday if they have been successful.
If they fail, Kompany will also miss the return leg against Liverpool as well as Premier League clashes with Wigan and Tottenham.
Pantilimon is also hoping to play again on Wednesday having so far been Mancini's choice in domestic cup competitions.
The 24-year-old Romanian knows, however, that England's Hart is very much the top man and is happy to carry on playing his part in a goalkeeping team that also includes Stuart Taylor.
He said: "The manager decides which 11 go on the pitch and I hope to be in there.
"We have both (Pantilimon and Hart) trained very well, and train for the team, to win trophies and all three goalkeepers are wonderful.
"The team is very good and we all want to be in this team."
City started confidently against United but were stunned when Wayne Rooney struck after 10 minutes and Kompany was dismissed soon after for a two-footed challenge on Nani.
They were still reeling from that double blow as Danny Welbeck hit a second and Rooney added a third from a penalty rebound.
Yet when it seemed like City might have to settle for damage limitation in the second half, they produced a rousing response and replied through Aleksandar Kolarov and Sergio Aguero.
United were left clinging on but City could not find an equaliser and their FA Cup defence ended at the first hurdle.
Pantilimon said: "We were surprised that the referee gave a red card after 10 minutes.
"At this level it is not normal and when you play a team like United it is important you have 11 men.
"But this is football and anything can happen. In the second half we played better, scored two goals and had a chance to get the draw."