The Chelsea boss insists the Nigerian is "fully focused" on playing football after the Blues lodged a formal complaint regarding the player and referee Mark Clattenburg
Earlier in the day, the Blues had lodged an official complaint against referee Mark Clattenburg over inappropriate language allegedly used by the official after the two sides' league clash on Sunday.
Chelsea didn't pursue claims that Juan Mata was also involved, with the Spaniard also featuring in the topsy-turvy Stamford Bridge clash.
“I spoke to my players in the last couple of days and made sure they were in the right frame of mind to play, so I had no concerns in picking the team I wanted to," Di Matteo told reporters.
“First of all we had both midfield players booked in the first half and secondly I wanted to change a little bit the team tactically.
“He’s [Mikel] fully focused on playing football. I wouldn’t have played him if I had any doubt.”
Chelsea looked to be heading for defeat until Eden Hazard struck in stoppage time, to net a penalty and take the game beyond 90 minutes, before further efforts from Daniel Sturridge and Ramires effectively killed off the tie and the manager was delighted with the spirit shown by his charges.
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Di Matteo added: "They showed a big, big heart, passion and pride to not want to lose this game.
"It was a very exciting game of football to watch, a typical cup game, quite open at times, and a lot of mistakes from both teams because there were a lot of young players involved in the game.
“I’m very pleased with the players that I picked tonight. They performed on a big stage like tonight and they’re going to play an important role in our season.
“We are trying to change a little bit the way we play and at times you’re going to make mistakes.
"But young players will learn from it and get better from it, and as a team we will get better as well in not making mistakes. But that’s the way we want to go forward.”
The Blues will face Leeds in the quarter-finals and Di Matteo is looking forward to the clash between the two sides, who have a storied past with each other.
“It’s always difficult to go and play away from home and Leeds and Chelsea have a little bit of history there," he said.
"I remember as a player playing against them too. It will be an interesting game to go and play at Leeds.
“He’s [Neil Warnock] got his style of football and he has to be respected. I think we’ll have plenty of time to think about that game.”