Di Matteo decided to leave experienced trio Frank Lampard, Didier Drogba and Michael Essien out of his starting line-up along with England striker Daniel Sturridge for the fifth round replay.
But he is adamant all the players are "on board" for the challenges they will face in the next two and a half months after starting the post Andre Villa-Boas era with a victory.
Di Matteo said: "We faced a difficult task today [Tuesday] given the events of the last couple of days and it was important for us to get through to the next round. We had to do a job today [Tuesday].
"Was it a brave selection choice? It was nothing to do with bravery. They were all on board. They know the targets we have to achieve.
"They are big players for this club. We have a squad and we have to utilise the squad. We have to try and get the best out of these players.
"It was a question of freshening up the team a bit, giving it some energy and fresh legs for a game like this. We had to fight today [Tuesday]."
Di Matteo, who is in charge for the remainder of the season, admitted: "It has been a difficult time.
"It's been difficult for the whole club. When events like this happen... we've lost a great guy (Villas-Boas).
"But you have to deal with it. Tonight [Tuesday] we had to focus on this game and move on as a club, put it to one side and move forward."
One bonus for Di Matteo was the return on the bench of skipper John Terry just two weeks after undergoing knee surgery.
Di Matteo said: "John has done very well and is determined to help the club, and we're pleased to see him. He's available.
"We have to take him with small steps because he's done well to come back in just over two weeks. But it was good to see him."
Di Matteo side-stepped questions over whether he would be interested in taking the role on a permanent basis - if offered the chance.
He said: "Would I take it? I'm very tired tonight [Tuesday]. I have to think about Stoke City from an hour's time onwards, and that's all I'm thinking about.
"Think whatever you want to think. I'm not thinking about anything else."
City boss Chris Hughton praised his team's efforts before being beaten by second half goals from Juan Mata and Raul Meireles in what was their 47th game of the campaign.
He said: "We gave it a real good go but needed to stay in the game at 0-0 longer in the second half. The first goal gave them a lift and the second was real quality.
"We have really enjoyed the cup runs in the Europa League and the FA Cup. People say they may have impacted on our hopes in the league.
"But I think they have had a positive impact on us and there is no shame in going out to a Chelsea side full of quality."