The Italian left Frank Lampard, Didier Drogba, Michael Essien, Gary Cahill and Daniel Sturridge out of his starting line-up and one of the players brought in, Salomon Kalou, scored the only goal in the second half at the Stadium of Light.
"We've been playing so many high-intensity games, Manchester City last week, Spurs on Saturday, and tonight was another one," Di Matteo told the club's website.
"It's a question of trying to energise the team and freshen it up. We knew Benfica played with a high tempo so we needed fresh players who could run.
"I'm involving everybody in the squad. I'm rotating, we need everybody until the end of the season."
Di Matteo was particularly pleased with Portuguese right-back Paulo Ferreira who started his first match of 2012 in place of the injured Branislav Ivanovic.
"Ferreira hasn't played for a while but he was outstanding," said the Italian.
FITNESS LEVELS
"We cannot play with only 11 players and you're going to see players who have played a bit less play more in the future because it's just impossible for us to play every three days and reach the fitness levels that are needed to win games."
Chelsea are also through to the FA Cup semi-finals and, occupying fifth place in the Premier League, are desperate to claw their way into the top four to earn a place in next season's Champions League.
Di Matteo said he was delighted with his team's victory at Benfica.
"It was an excellent performance," he added. "It's difficult to play against Benfica, they haven't lost here for a couple of years [in Europe] and we saw why.
"They are a good side with good individual players and a threat from set plays. I always felt we looked solid defensively, well organised and I always fancied us to score a goal."
Benfica defender Maxi Pereira said the tie was far from over.
"We played a good match tonight and I think we can win in London," he said. "A lot could happen and it is not over yet."
The second leg at Stamford Bridge is on April 4. The winners will meet Barcelona or AC Milan in the semi-finals.
