A goal in each half of the final from Modric and Benzema was the difference as Madrid comfortably defeated last year's champions to reinforce their status as the top team in Spain this season.
Madrid have already beaten Barcelona twice - including in the Super Cup semi-finals - and Atletico Madrid once, and are more than 15 points clear of both rivals halfway through the La Liga campaign.
Madrid's 12th Super Cup title moves them only one behind Barca, the competition's most successful team.
It was Madrid's second Super Cup title since the competition was controversially moved to the Middle East in 2020 and played in a revamped "Final Four" format.
Modric opened the scoring with a curling shot into the top corner after being set up by forward Rodrygo just inside the area in the 38th minute.
Captain Benzema added to the lead by converting a 51st-minute penalty kick after a handball determined by video review.
Athletic had a chance to move closer in the final minutes but Madrid goalkeeper Thibaut Courtois saved Raul Garcia's penalty.
Madrid defender Eder Militao was sent off for the handball that prompted the penalty.
