Brazilian duo Alex Teixeira and Fernandinho grabbed the goals for the hosts on Tuesday evening before a late consolation strike from their compatriot Oscar gave the travelling fans something to cheer.
And, despite Shakhtar now sitting three points ahead of Chelsea at the top of Group E, Di Matteo feels his side can seal qualification for the knockout stages in their upcoming games at Stamford Bridge.
He told reporters: “We must win our two Champions League home games and I'm confident it will be a different game for Shakhtar [at Stamford Bridge].
“We're strong at home as well.”
The Italian also rued his side's sluggish start in comparison to their opponents, adding: "The early goal helped Shakhtar massively and it unsettled us. We were getting better in second half but then got caught.”
The former Blues attacker was quick to highlight the quality his side faced, however, with Shakhtar going into the game on a 27-match unbeaten run.
"I think we have to just look at this performance as a single one," he told Sky Sports.
"They [Shakhtar] are a very strong team and they showed that again tonight. It's a difficult group we are in and the Champions League is always very competitive.
"You look at the other result in our group and it shows just how competitive it is.”
Di Matteo was also keen to dismiss suggestions that John Terry had been distracted by his recent domestic ban for racially abusing Anton Ferdinand, despite a below-par performance from the defender.
"I think the commitment from our players was 100 per cent,” he affirmed. “Probably we could have done better as a team, but he [Terry] was alright. I don't think he was affected by it [the off-field problems]."
Frank Lampard picked up a knock during the match and the 42-year-old confirmed the midfielder has suffered a recurrence of the calf problem sustained against Norwich earlier in October.
"It's the same calf that he has had for the last two-and-a-half weeks,” he added. “He was fine [before the match] but it went in the game."