The England international was bamboozled by a Luis Suarez nutmeg prior to the opener before his slip allowed Jordan Henderson to put the Reds two in front.
The 31-year-old also came in for heavy criticism recently following his red card in the Champions League semi-final against Barcelona, for kneeing Alexis Sanchez in the back.
However, Di Matteo praised Terry's leadership in the past, telling reporters: "John has been magnificent for us.
|Luiz and Cahill doubts for Munich
"He has been playing all the games, he has been a leader and everything you want in a captain."
Though defeat to the Reds ended Chelsea's hopes of a top-four finish, they can take England's fourth Champions League place for next term by defeating Bayern Munich in the competition's final on May 19.
However, Di Matteo will be without Terry for that game - as one of four players suspended - and potential replacements Gary Cahill and David Luiz are battling to be fit in time.
"We are working towards their fitness and trying to get them back as soon as we can, but I can't answer the question,” he added.
"They were not available for Liverpool so we will have to see.
"We have injuries, we had five players unavailable and we need to see how the players are after the game as well.
"We will check on their progress and how they will develop. I would like to have everyone available. I will have to think about the team as we have those suspensions.
"I have to think about how they play and which players fit best into our set-up for the final."