Jose Callejon gave an under-strength Real side the lead in the 30th minute and, after defender Raul Albiol was sent off in the 70th, Ronaldo responded to criticism of his performance against Barca by sprinting clear to notch the second goal.
The Portugal forward barely celebrated with a grim look on his face, and was substituted after a subdued showing minutes later, to a mixture of whistles and applause.
"Cristiano is fine, he is an extraordinary player," Real sports director Miguel Pardeza told Spanish television when asked how Ronaldo was handling some negative press.
"If something marks him out from many other players it is that he never gives up on a chance to play, and always gives his all whatever the circumstances.
"No one should doubt his commitment, his personality or his abilities as a player."
The only upset on the night was Levante, who are fourth in La Liga, losing 3-1 at recently relegated Deportivo La Coruna, and second division Cordoba beating local top flight rivals Real Betis 1-0.
The 2008 Cup winners Valencia and misfiring Villarreal were held at third tier Cadiz and Mirandes respectively, while Real Zaragoza and Espanyol drew away to second division opponents.
La Liga strugglers Racing Santander, in the hands of a temporary coaching trio, came back from 2-1 down to snatch a 3-2 win at home to Rayo Vallecano with a double from Christian Stuani and a late strike from fellow Argentine Ariel Nahuelpan.
MINING TOWN
An early Frederic Kanoute strike gave Sevilla a 1-0 win at third tier San Roque while Malaga and Sporting Gijon won by the same scoreline over Getafe and Real Mallorca respectively.
Xabi Prieto netted twice as Real Sociedad thumped Granada 4-1 and Osasuna were 3-1 winners at Almeria, who finished with nine men. The second legs are scheduled for next week.
A steady rain fell on a packed stadium in the old mining town of Ponferrada, but hopes of an upset against nine-times European champions Real soon disappeared.
Jose Mourinho's side were still smarting from their 3-1 home defeat by Barca on Saturday and, although weakened, included players such as Kaka, Gonzalo Higuain and Ronaldo.
Callejon fired Sami Khedira's cross into the top corner to put the visitors ahead but Ponferradina, who play at the same level as Real Madrid's youth team, did not cave in.
The hosts ran their socks off. Yuri saw an impressive overhead kick fly straight at Real keeper Antonio Adan and Luis Domenech struck the bar just after the break.
Albiol picked up a second yellow card to leave Real with 10 men but they rea
