Real took the lead in the 38th minute after Rodrygo sprinted past two defenders before passing to Modric, who rifled a shot into the back of the net.
Benzema extended their lead in the second half with a penalty after the video assistant referee spotted a handball from Yeray Alvarez inside the area.
Real were reduced to 10 men three minutes from time after Eder Militao was sent off for a goalline handball.
"You can never get tired of winning," Modric told a news conference.
"I enjoy the same every title, when you play at Real Madrid you have to win. It's part of the DNA of this club. Fans expect the most of you. So now we have to look forward to win more and again in the next months."
After two exciting semifinals, the final was a one-sided encounter, with Real Madrid completely dominating and never facing any real danger.
Real enjoyed the great majority of support from the 30,000 fans in the King Fahd Stadium, which was at 50% capacity due to the COVID-19 pandemic.
France striker Karim Benzema had the backing of the Saudi supporters, but it was Modric's night.
"As I've reached a certain age, and people talk a lot about ages in football, but I'm enjoying it more than ever," Modric said. "I've always enjoyed it, I love what I do, but now I enjoy it even more because you never know how long you'll last at this level.
"I'm doing everything to keep going for a few more years. I make an effort, and there's nothing better for me than being a Real Madrid player, enjoying every day and winning trophies. It's 18 now in nine-and-a-half years and I hope more will come."
Carlo Ancelotti had said in the buildup to the game that his side were the very essence of a counter-attacking team and on Sunday Modric and forward Rodrygo would have made their coach proud, with a perfectly executed counter to open the scoring.
"I think with the two games we played here, we were the team that deserved the trophy," Ancelotti said after the match. "We played two different games and won both. Today demanded a different type of game, we controlled it for 70 minutes with possession, then we dropped off a bit but that can happen in a final. It's deserved, we're happy and we'll keep going."
Benzema has made a habit of scoring against Athletic and doubled the advantage from the spot with his 18th goal in 26 games against the Basque side, the most he has scored against one team in his career.
It was the 12th time Real had won the Spanish Super Cup, having claimed both editions of the competition in Saudi Arabia. Last year's edition, won by Athletic, was held in Spain due to the pandemic.