The world player of the year headed in after 26 minutes for his 73rd Champions League goal with Real's first chance and he set up Marcelo to make it seven wins for the Spanish side in seven Champions League games this season and 10 in a row.
Real's victory was nowhere near as emphatic as last season's 6-1 romp at Schalke at the same stage of the competition but it was a much-needed confidence boost for Carlo Ancelotti's team after a lacklustre start to the year in Spain.
"Anything can happen in the Champions League. We are humble and we know that to get through we have to work hard like we did today," Marcelo told Spanish television. "We have a two-goal advantage but the tie is not over.
"Cristiano is not obsessed with scoring. Goals come when the team works together," he said of his team mate.
Looking to become the first team to retain the Champions League title, Real, eliminated from the King's Cup this month and crushed 4-0 by Atletico Madrid in La Liga, host Schalke in the second leg on March 10.
The Germans fielded five defenders and were on the back foot from the start but coach Robert Di Matteo's disciplined 5-3-2 system proved effective.
Schalke gradually grew in confidence and created good chances for Dennis Aogo and Klaas-Jan Huntelaar.
But Ronaldo put Real ahead, ending his mini lean spell with a glancing header from Daniel Carvajal's cross to take his competition tally to 73, two short of the record held by Barcelona's Lionel Messi.
Schalke keeper Timon Wellenreuther, making his competition debut, did well to deny Karim Benzema and Ronaldo, parrying a curling free kick in the 34th.
Schalke's game plan collapsed when Huntelaar, back in action despite serving a suspension in the Bundesliga for a red card, limped off with a leg injury.
Real were almost punished by 19-year-old Felix Platte who replaced Huntelaar and struck a shot against the crossbar 15 minutes from time.
"The quality made the difference," Schalke coach Di Matteo said.
"They have superb players and that is why they are the title holders. They had one chance and scored two goals."
Brazilian Marcelo ended any lingering German hopes with a powerful shot 11 minutes from the end after good work from Ronaldo to keep Real firmly on course for a record-extending 11th triumph in Europe's premier club competition.
(Reporting by Karolos Grohmann, Additional reporting by Emma Pinedo in Madrid, editing by Ed Osmond)
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