The Portugal international, whose midweek hat-trick against Sweden secured his country's passage to the 2014 World Cup in Brazil, had opened the scoring for Real in Andalusia after only three minutes.
His withdrawal raised fears about his availability for Real's Champions League game with Galatasaray on Wednesday.
But, after being replaced by Jese Rodriguez early in the second half due to a muscle strain, Ronaldo insisted the injury was a minor one.
"It was a precaution," he told the club's official website. "It was nothing special. They gave me a kick in the first half and I felt the muscle was a bit stiff."
Real manager Carlo Ancelotti did not appear to be overly concerned but revealed the full extent of the injury will be confirmed on Sunday.
"I don't think it is serious because he is not in pain. It is a muscle strain so I hope he will be fine soon," said Ancelotti after the game.
"Tomorrow there will be more tests, but we don't think it is a big problem."
Real's five-goal haul against Almeria took their goal tally to 20 in their last four league outings.
Gareth Bale was again on the scoresheet for Real, scoring his fourth goal in five matches for his club.