Di Matteo played down comparisons between Malouda's segregation and those of Nicolas Anelka and Alex last season, which arguably contributed towards Andre Villas-Boas' downfall as manager.
"They have accepted the decision that has been made by us, and they're just going to focus on their targets for this season," Di Matteo said.
Chelsea's squad were said to be angered by what was seen as an attempt by Villas-Boas to assert his authority, with his successor subsequently praised for the way he brought other outcasts back into the fold.
But Di Matteo got tough last week when he and the club decided to banish Malouda to the Blues' under-21 team following the France winger's refusal to accept several offers to move on despite having apparently expressed a desire to leave.
Malouda, whose contract expires next summer, vented his frustration by revealing the news on Twitter but did not succeed in mobilising his team-mates, according to Di Matteo.
He continued: "Over the past, there's been some expression of the player to part company, but it hasn't happened. So we've moved forward, brought in other players and they're the ones we're going to work with this season. It was a combined decision between me and the club.
"It's obviously not an extremely positive message or decision for him, but I guess, at the end, we have to look after our own interests and that's the decision we've taken."
Despite his banishment and omission from Chelsea's squad for the group stages of the Champions League, Malouda was included in the club's submission for the first half of the Barclays Premier League season.
Asked if he had played his last game for the European champions, Di Matteo added: "I don't know, only the future will tell. But he's with the under-21s. The transfer window doesn't open again until January."
Source: PA
Source: PA