Karim Benzema's 19th-minute strike at the Bernabeu saw the La Liga giants take the upper-hand in the UEFA Champions League semi-final.
Guardiola seemed surprised by the speed of Real's counter-attacks, and said Carlo Ancelotti's men would be hard to beat if allowed to play on the break.
"The faster the ball goes, the faster it comes back," he told Canal+.
"We controlled the game but Real Madrid were waiting to counter-attack. And on the counter-attack they are unstoppable.
"They have great athletes and if you allow them to run, they will take advantage."
Guardiola paid tribute to Real, but said there was still a long way to go with the second leg to be played on Tuesday.
"Congratulations to Madrid. They won in the first 90 minutes and now we have another match to play in Munich," the former Barcelona coach said.
"They have a lot of legs, they are the best team in the world on the counter-attack. We wanted to control the match with possession.
"We failed to score, but there's another game and we'll give our all."
Guardiola was particularly pleased with his side's first-half display, but said Real showed their quality to still create chances.
"In the first half, Real Madrid didn't string together three passes. They didn't have the ball," he said.
"When they did have the ball, they created danger.
"I'm proud of my team, they showed a lot of strength against one of the best teams in the world and we can still bring it in the second leg."
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