The Chelsea forward escaped a booking for an ugly challenge in the opening stages of the Blues' 2-1 victory over Liverpool on Sunday, going on to score the winner.
The Cameroon striker appeared to rake his studs down Henderson's knee in the early stages of Chelsea's 2-1 triumph, with referee Howard Webb awarding a free kick but deciding not to show a card for the challenge.
Eto'o further piled the misery on Liverpool by scoring the winning goal in the first half, after side-footing home Oscar's center.
The 32-year-old now concedes that he deserved punishment for the challenge on Henderson, and he has apologized to the England international.
Speaking to The Sun, he said: "Maybe I should have been sent off. But I'm not the referee. Everyone is entitled to their opinion but we must respect the decisions from the officials. During the match in the first moments, the game was passionate on both sides, but people know I'm not violent.
"I was really sad to see Jordan [Henderson] on the floor - I want to take this opportunity to say sorry."
The former Barcelona and Inter forward was involved in further controversy in the closing stages of the match, when he appeared to cut across Luis Suarez in the penalty area, with the Uruguayan chasing down Cesar Azpilicueta.
Liverpool manager Brendan Rodgers felt that his side should have been awarded a penalty for the challenge, but Eto'o is adamant that Webb made the correct decision.
"'The ref did his job," he said. "He was two meters away from us. We can't all be the ref and it's easy for people to talk when they are far away. Yes, there was contact, but I didn't commit a foul."