The 28-year-old opened the scoring before being forced off with a thigh problem, but goals from Karim Benzema, Gareth Bale, Isco and Alvaro Morata secured an emphatic win
Fresh from inspiring Portugal to World Cup playoff glory against Sweden with a phenomenal midweek hat trick, Ronaldo gave Real an early lead with his 25th club goal of the campaign.
Karim Benzema marked his 200th Madrid appearance with a beautifully-struck second before Gareth Bale, Isco and Alvaro Morata added deserved late gloss to the scoreline.
But Ronaldo provided the story of the second half nine minutes in, walking gingerly from the field with a suspected thigh problem after coming off second best in a challenge with Aleix Vidal. The Portugal star must now be considered a doubt for the midweek Champions League match against Galatasaray.
Asier Illarramendi was selected in midfield for Madrid as a result of Sami Khedira's long-term knee injury absence, while Isco returned to the starting XI in support of the fearsome attacking trio of Ronaldo, Bale and Benzema.
Almeria coach Francisco Rodriguez welcomed back Verza from suspension and picked Helder Barbosa in place of Fernando Soriano as his team chased a fourth consecutive victory.
Ronaldo handed the visitors the lead when, having already seen a shot deflected behind, he supplied a deft touch to direct Isco's excellent right-wing cross low into the far corner after three minutes.
Home goalkeeper Andreas Esteban then did superbly well to beat away a viciously swerving Ronaldo drive and was up quickly to block Benzema's follow-up.
Angel Trujillo denied Ronaldo with a superb last-ditch challenge in the 18th minute before Suso cut in from the left to curl a shot wide – Almeria's most promising attacking moment of a half it grew into.
Real full back Daniel Carvajal raced into the area to collect Xabi Alonso's magnificent raking ball in the 50th minute but Esteban produced another fine stop before Ronaldo's match ended early.
Bale should have taken the edge off manager Carlo Ancelotti's concerns in the 57th minute when he blazed over from close range after Isco sent Carvajal marauding down the right.
Diego Lopez was forced into a sharp save of his own in the Madrid goal when Suso's low free-kick evaded the defensive wall but Benzema would hand the visitors breathing space after the hour.
Ronaldo's replacement Jese Rodriguez drove at the Almeria defense and fed Benzema, who shifted the ball on to his right foot to send a rasping 20-yard drive beyond Esteban.
Bale headed Alonso's 67th-minute corner over but capitalized on a lapse from Sebastian Dubarbier to find the net four minutes later.
Isco was the provider on that occasion and got the goal his endeavors deserved with a wonderful clipped finish from the edge of the are before Morata – on for Benzema – raced clear of an embattled Almeria back line to chip Esteban.
There was almost more late misery for the hosts when Casemiro crashed a 25-yard drive against the post before the final whistle confirmed a cut in Barcelona's advantage over its great rival to six points.
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