Terry was an unused substitute against Shakhtar Donetsk in midweek, causing something of a stir given the fact that the skipper had missed four games recently during his domestic ban.
But Di Matteo insists Terry's future at the club is secure and claims the defender accepted his decision.
"There are no question marks or doubts at all about John's long-term future here as a player and as a captain, and the leadership he brings in the dressing room," said Di Matteo.
"He has been very supportive with the players who were playing. It's never easy to tell a player he's not going to start a game but, as a player, you respect the manager's choice.
"You might not always agree, but if he tells you an honest opinion that he believes it's better to start with a different player for tactical reasons or whatever reasons, you respect that."
Having retired from international football, Terry will link up with the youth team for training over the next week with many of the senior players away from Chelsea's Cobham base.
"We usually join up the small group that remains with the youth team so we get a good look at the youth players as well," added Di Matteo.
"Normally it's more youth players than seniors. We'll have three or four senior players max. It's great for the youth team players to train with someone such as JT."