An own goal by goalkeeper Diego Marino and a stoppage-time strike by substitute Isco ensured Real kept a firm grip on third place in La Liga.
Barcelona, who visit Rayo Vallecano on Thursday, hold a five-point lead over second-placed Atletico who triumphed 3-0 at home to Real Sociedad on Tuesday.
Real, nine points off the pace, are four points in front of fourth-placed Villarreal who drew 0-0 at Celta Vigo on Wednesday.
Zinedine Zidane's Real were missing Sergio Ramos and Marcelo in defence, although Pepe returned after a long injury layoff, midfielder Luka Modric and striker Karim Benzema, replaced by teenager Borja Mayoral making his first start.
Ronaldo put them ahead in the 34th minute with his 23rd league goal of the season after Levante left back Lucas Orban tripped Lucas Vazquez.
Real went further ahead in the 38th minute when a shot by Mayoral came back off the post, hit the diving Marino's back and went over the line.
Bottom club Levante hit back from the restart with Giuseppe Rossi setting up fellow striker Deyverson who slotted his eighth league goal of the season.
Isco completed the win two minutes into stoppage from a Ronaldo pass.
Ronaldo missed two good chances in the second half, the first following a superb lofted pass on the left from which he hit the inside of the post.
Keylor Navas made good diving saves from Rossi in the fifth minute and substitute Ruben Garcia near the end.
(Writing by Rex Gowar; Editing by Tony Jimenez)
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