The French star scored either side of a Franco Cervi strike after Santi Mina had given the visitors the lead on four minutes.
Vinicius Junior added a third for Real before teenager Eduardo Camavinga scored six minutes into his debut.
Benzema sealed his hat-trick with an 87th-minute goal as Carlo Ancelotti’s side moved top of La Liga.
Despite ongoing construction work, 30,000 supporters were welcomed back to the Bernabeu.
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As Los Blanco played their first match there since beating Barcelona in El Clasico on 1 March 2020.
The victory moves Real to the top of the table on goals scored.
They are on same points with Valencia and Atletico Madrid.
