The France striker hit home 13 minutes from time to deny the plucky hosts their first point in the competition following a superb display of determination from the Bulgarian side.
Georgi Dermenzhiev's men had come within a last-minute penalty of taking a point from Liverpool in their opening fixture and once again belied their tag as Group B's underdogs on Wednesday.
The hosts took the lead early in a clash moved from Razgrad to the Stadion Vasil Levski in Sofia through forward Marcelinho.
Dermenzhiev's side were rewarded for a fast start to proceedings in the sixth minute as Marcelinho took advantage of Real's continued failings at set-pieces.
The Brazilian nodded in at the far post after Cosmin Moti had flicked Fabio Espinho's corner into his path in another display of poor marking from the visitors.
But Ronaldo's spot-kick was a poor one, allowing Vladislav Stoyanov to preserve Ludogorets' advantage with a save down to his right.
Ludogorets remained a threat going forward, though, and Real were grateful to captain Iker Casillas for keeping them level with a strong save on the half hour from Mihail Alexandrov.
Real's superiority was apparent by the end of the half but Ancelotti's men continued to be profligate in front of goal, Hernandez dragging an effort wide three minutes before half-time, with Stoyanov then brilliantly denying Bale seven minutes after the restart.
For all Real's pressure, Casillas was just as busy at the other end, the Real captain producing flying saves from Espinho and Marcelinho.
However, Ludogorets admirable resistance was finally ended as substitute Benzema - brought on for Hernandez - rescued Real by volleying home Marcelo's left-wing cross and a frustrating outing could get worse for the holders, who saw Ronaldo pick up a late ankle injury.
