Di Matteo admitted he took a risk with his team selection, which saw him leave out Napoli heroes Frank Lampard, Didier Drogba and Michael Essien and hand rare starts to Paulo Ferreira, John Obi Mikel and matchwinner Salomon Kalou.
"It's just a question of trying to energise the team, freshen up the team," Di Matteo said.
"We knew Benfica play at a high tempo so we needed fresh players who could run. That was the reasoning behind it."
The match was the third of seven in 20 days for Chelsea.
Di Matteo said: "I'm involving everybody that is in the squad, rotating. We'll need everybody until the end of the season.
"Paulo Ferreira hasn't played for a while but was outstanding. We cannot play with just 11 players. We need everybody in the squad.
"You'll see other players who have maybe played a little less in the past paying more of a role in the future.
"It's just impossible for us to play every three days and reach the fitness levels needed to win games."