Los Blancos beat Liverpool 3-1 in Kiev last weekend to claim the trophy for the third season running and the fourth time in five years.
Guardiola, whose City side were knocked out at the quarter-final stage by finalists Liverpool, believes that Zidane and Madrid deserve huge credit for what they have achieved.
"It's spectacular, you have to take your hat off to them," he said at an event for the Johan Cruyff Foundation. "It doesn't matter if they deserve it or not, because it's very difficult to do what they've done.
"They've demonstrated their quality, and we hope to prevent them from taking the fourth consecutive one. Zidane has done a spectacular job."
Madrid now have a chance to defend their UEFA Super Cup crown when taking on Europa League winners Atletico Madrid in Estonia early next season.