The Portugal forward, who had set up Sergio Ramos to head the opener for his side in the 31st minute, helped turn the game back in his side's favour after Almeria had fought back to 2-2 in the second half.
In the 81st minute, he won a disputed penalty after he tumbled over Almeria goalkeeper Diego Alves in the area.
Alves saved his spot-kick but Karim Benzema netted the rebound to make it 3-2 to the hosts. Ronaldo did not celebrate with his team mates as he trudged back to his own half alone.
"I was angry with myself. I missed a penalty," he told reporters.
"I don't like to lose or to fail, I am a perfectionist. But I don't give up either and I was pleased for Karim's goal."
Two minutes later, Gonzalo Higuain crossed for Ronaldo to score, his first goal since returning after two months out with an ankle injury.
In his exuberant celebration he ripped off his shirt earning his first yellow card.
He picked up his second yellow in the last minute of the game after reacting to a provocation, kicking Almeria's Juanma Ortiz on the leg.
"It was an instinctive reaction, I know I made a mistake but I am human," he said. "These things happen in football but I have to learn from it.
"I have asked for forgiveness from my colleagues."
Ronaldo misses the trip to play title-rivals Valencia next weekend.
Real coach Manuel Pellegrini defended Ronaldo, saying: "His sending off his was perhaps fair by the letter of the law but he's the type of player who doesn't deserve to be sent off.
"He focuses on creativity and playing football, it's others who dish out the kicks. The red card was avoidable but it's a one-off and that's that."
