Benzema, 22, had previously managed just three goals in all competitions this season and was behind Gonzalo Higuain in the pecking order under new coach Jose Mourinho.
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The former Olympique Lyon player, in his seventh start of the campaign, took his chance with aplomb at the Bernabeu as a second-string Real brushed aside Auxerre.
Ronaldo also chipped in with a goal, his 20th of the season in 21 matches in all competitions.
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Auxerre's efforts were in any case in vain as Ajax Amsterdam's 2-0 victory at AC Milan secured third position in Group G for the Dutch side and a spot in the Europa League.
Nine-times European champions Real had already won the group, with second-placed Milan also assured of a place in the last 16.
Ronaldo, one of three regular first-teamers in the suspended Mourinho's starting 11, crossed for Benzema to nod in the opening goal in the 12th minute.
The Portugal winger lashed home the second in the 49th after Marcelo's fine through ball sent him clear and Benzema netted in the 72nd with a low shot.
He then intercepted an attempted clearance by goalkeeper Olivier Sorin before lifting the ball into an empty net to complete his treble just before the end.
"I am very pleased to have scored three goals," Benzema told Spanish television. "I am feeling better every day and that is being reflected on the pitch.
"I am going to work hard to play like I have done today all the time."
POOR RUN
Real are looking to end a poor run in Europe's elite club competition during which they have failed to make the quarter-finals the past six seasons despite investing heavily in players and coaching staff.
By winning the group they should avoid another heavyweight club when the draw is made on December 17 and their performance in the group phase, with five wins and a draw, was their best in the Champions League.
Benzema's opening goal was the club's 300th since the Champions League was created in 1992/93, the first side to reach that total.
Auxerre, who beat Ajax at home in November, finished bottom of the group with three points and coach Jean Fernandez said his team had suffered with injuries in a group of former champions he knew would be tough.
"I said before that Real have what it takes to win the competition and I would say that they are one of the favourites," said Fernandez.
"Our priority now is to play a good (French) league campaign and secure our place in the first division," he added of the 13th-placed team.
Real's reserve goalkeeper Jerzy Dudek had a mixed night, making two excellent saves to deny Jean-Pascal Mignot and Dennis Oliech in the first half before going off after getting a bang on the head in a collision with Roy Contout.
The former Liverpool keeper, who rarely gets a chance to replace first-choice Iker Casillas, was given a standing ovation as he left the pitch and Auxerre hardly troubled his replacement Antonio Adan.
Mourinho, who left Champions League holders Inter Milan at the end of last season, watched from the stands after being suspended followi
