Real now lead second-placed Barcelona by four points after the Catalans paid a heavy price for the absence of Lionel Messi and Luis Suarez in a 0-0 draw with nine-man Malaga earlier on Saturday.
Ronaldo struck the decisive spot-kick as Real edged Atletico on penalties in the Champions League final in May and was the match winner once more, albeit with a slight hint of fortune.
The Portuguese's opener took a wicked deflection on its way past the excellent Jan Oblak.
"We played an enormous game from the start against a very difficult opponent," said a delighted Madrid boss Zinedine Zidane.
"There are very few teams that can come here and win 3-0."
A third league defeat in four games leaves Atletico's title ambitions in tatters in their final season at the Calderon.
Diego Simeone's men are now nine points adrift of Real down in fifth.
"Above all in the first-half they were better than us," admitted Simeone.
Real were without six key players in captain Sergio Ramos, Pepe, Casemiro, Toni Kroos, Alvaro Morata and Karim Benzema, but impressively controlled the first 45 minutes.
Only an incredible save by Oblak prevented Ronaldo opening the scoring with a towering header on 12 minutes that the Slovenian somehow clawed away low to his left.
Oblak made another smart save to deny Luka Modric moments later, but he was helpless for the opener as Ronaldo's free-kick was deflected behind him via the Atletico wall.
Yannick Carrasco curled inches wide from the edge of the area before Antoine Griezmann blasted a shot across goal with no Atletico player waiting to knock to the ball into an unguarded net.
However, any hopes of an Atletico fightback were punctured when Stefan Savic upended Ronaldo inside the area and the three-time World Player of the Year dispatched the resulting spot-kick.
- Messi missed -
================
At the Camp Nou, Barca were held scoreless for the first time in La Liga since Malaga's visit in 2014 without the ill Messi and suspended Suarez.
Without his usual two strike partners, the focus was on Neymar to break down the mass ranks of Malaga defence.
The Brazilian fired into the side-netting inside the first 10 minutes, but Barca's bright start quickly fizzled out.
Indeed, Juan Carlos had the best chance of the game for Malaga just before the hour mark when he rounded Barca 'keeper Marc-Andre ter Stegen but fired into the side-netting with the goal gaping.
Yet, even with a man advantage, Barca badly missed the creativity of Messi and injured captain Andres Iniesta as they resorted to launching cross balls into Gerard Pique, who moved forward from central defence to act as an emergency forward.
Barca's best chance came deep into stoppage time when Carlos Kameni somehow clawed Neymar's header from point-blank range to safety before Carlos was also dismissed.
Sevilla moved up to third as they produced a stunning fightback from 2-0 down to win 3-2 at Deportivo la Coruna.
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