Gunners counterpart Arsene Wenger claimed play should have been stopped for a free-kick to his team in the build-up to the opening goal, and that Chelsea were also awarded a soft penalty when Ramires went down in the box.
But Benitez said: "We deserved to win. The team were doing really well. You can analyse every incident.
"The team were very good in the first half, and defended with character in the second half."
Benitez insists he had no concerns when Arsenal pulled a goal back through Theo Walcott, despite seeing Chelsea surrender a two-goal advantage in midweek against Southampton at Stamford Bridge.
"I think we were creating a lot of chances at home in the last few games, but not winning. We were controlling the games and doing well," Benitez added.
"But today we had a lot of chances in the first half, were on top of them, controlling the game.
"Even in the second half, we had situations on the counter-attack where we could have scored another."