Goals from Jose Antonio Reyes after 62 minutes and Sergio Aguero after 83 gave the Europa League winners an easier than expected win over the Italians who won the treble last season when they added the Champions League to their domestic double.
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Although defeat in the traditional curtain-raiser to the European club season is no calamity, Inter looked poor and Benitez admitted his new team needed to improve if they wanted to have any hope of repeating last season's successes.
"We started the game well with two or three chances and then we lost control. At the end it was too open," Benitez told RAI television.
"The tactics are not quite there, we've got to work harder. Today we've not seen the team we want."
Aguero told Spanish television: "It was nice to score but it's the team performance that counts and I hope we can carry it on into the league."
Reyes, who worked tirelessly alongside Diego Forlan up front for the spirited Spaniards and was named man of the match, added: "We have a great team and great supporters and have proved we can win titles."
Inter's disappointing night was completed when Diego Milito, who scored both goals when his side beat Bayern Munich in the Champions League final in Madrid in May, saw his 90th-minute penalty saved by Atletico keeper David de Gea.
Atletico's victory means that the winners of UEFA's secondary competition now lead the European champions 18-17 overall in Super Cup finals.
Samuel Eto'o looked out of sorts up front and the dynamism of Wesley Sneijder was lost with him playing in an unfamiliar advanced role.
Sneijder went close in the opening minute with an angled shot over the bar and Eto'o had two efforts that went wide, but it was Atletico who looked more likely to score as the second half progressed.
