Ronaldo secures Real Madrid's Cup semi-final spot
Real will tackle holders Sevilla in the last four while Barcelona, who saw off Real Betis 6-3 on aggregate, despite losing the second leg of their quarter-final 3-1 on Wednesday, will meet Almeria.
Almeria had seen off Deportivo La Coruna 4-2 on aggregate in their last eight encounter.
Ronaldo, the Spanish League's top scorer, found the target in the 23rd minute from eight yards.
Xabi Alonso created the goal with a sweet, crossfield pass to Sergio Ramos who in turn found the unmarked Ronaldo.
Atletico, last year's runners-up, were desperately disappointing and created few chances on their home ground having lost 3-1 in the first leg last week.
Fran Merida had Atletico's best opportunity but fired weakly into the arms of Real goalkeeper Iker Casillas in the 51st minute.
Real's win came just hours after general manager Jorge Valdano Thursday denied reports of a rift between him and coach Jose Mourinho.
"I have no problems at all with Mourinho," the Argentine told reporters.
"Crazy things are being said. All this commotion that has happened in recent days doesn't make any sense," he said, according to sports newspaper AS.
"Since Sunday, we have had dinner together… We speak constantly, we messaged each other just yesterday."
Rumours of friction between the two were fueled by comments Valdano made after Madrid's shock 1-1 draw against bottom club Almeria on Sunday, a result which left them four points behind league leaders Barcelona.
The general manager said French striker Karim Benzema, who spent the much of the match on the bench, was suffering "a great injustice".
Real Madrid are on the hunt for a new striker to replace injured Argentine Gonzalo Higuain, who could be out for the rest of the season, but Valdano is reportedly pushing for Benzema to start alongside Cristiano Ronaldo up front.
On Wednesday, in what was interpreted as a rebuke to Valdano, Mourinho said he had spoken about the need for a new striker in November when it was obvious that Higuain would be out for some time.
But Valdano Thursday said his post-match comments were misunderstood.
Mourinho "interpreted that phrase as a message (to him) but that was not my intention."