Los Blancos claimed all three points at the Estadio Alfredo Di Stefano after Benzema netted a second-half brace either side of Marcos Asensio's 74th-minute strike.
In doing so, the former France international climbed to fifth place on the club's all-time leading goalscorers list with 243 goals across all competitions, overtaking legendary forward Ferenc Puskas in the process.
The result also saw Zidane become the coach with the second-most wins in Real Madrid's history, with the 47-year-old having now overseen 133 victories in just 201 matches across his two managerial spells with the club.
However, the Frenchman is still some way behind all-time leader Miguel Munoz, who led Real to an incredible 357 victories across two spells of his own.
10. Rafa Benitez (Dalian Yifang) - €13m
9. Maurizio Sarri (Juventus) - €13.5m
8. Fabio Cannavaro (Guangzhou Evergrande) - €14m
7. Ernesto Valverde (FC Barcelona) - €19m (Before sacking)
6. Zinedine Zidane (Real Madrid) - €23m
5. José Mourinho (Tottenham) - €23m
4. Jürgen Klopp (Liverpool) - €24m
3. Pep Guardiola (Manchester City) - €27m
2. Antonio Conte (Inter Milan) - €30m
1. Diego Simeone (Atlético de Madrid) - €40.5m