But Chelsea committed more than twice as many fouls as the Catalans and Guardiola believes the visitors should be punished for playing a negative game.
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"I don't complain about the referees, but I think the referee should see which team is attacking and which team is interrupting the play.
"We play clean; we foul as little as possible. And we have the same amount of cards as them. It's not normal, it's not fair.
"We said before the game: 'no hard tackles, no fouls, it's not necessary', but we attacked, attacked and attacked and it's ridiculous that we should end up with the same amount of cards as them."
Guardiola believes such decisions could decide games in elite European competition.
"In the Champions League, small details decide games and could be the difference between winning or losing the tournament," he said.
"Those things didn't go our way tonight - Chelsea were constantly interrupting play with fouls while we played our normal attacking game," he said.
"One team is playing an attacking game and that should be taken into account.
"Yaya's card (for dissent) was scandalous and I can't understand it - the referee should see which team is looking to attack," he added.
Nevertheless, Guardiola said he was not unhappy with the result.
"The result is what it is. Chelsea played very defensively today, they were very disciplined and very strong with six players defending," he said.
And the Barca coach vowed to attack at Stamford Bridge.
"We will go to London and to the Bernabeu (for Saturday's Primera Division game against Real Madrid) with the same spirit," he said.
Puyol will miss the second leg after picking up a card, while Rafa Marquez is sidelined for the rest of the season after breaking down early in the second half.
"Rafa's loss is the worst thing about today but it will make us stronger," Guardiola said.
"He's sad and we'll try to lift him - it's a meniscus problem and we'll do tests, but he'll be out for the rest of the season," he added.
Despite the absence of those two in defence, Guardiola still believes his side can make next month's final in Rome.
"They are very important players, but we'll play with others.
"We want to get to the final and we'll find a solution for it.
"We'll rest and go out and win the game. I don't know what will happen," he said.
However, the Barca coach knows his side will have an uphill task if Chelsea play the same way in London.
He said: "We love to win and love to score. We will be strong.
"It's never easy to play against Chelsea, they are a very good team.
"We played a good game, we were just missing a goal. It's never easy when your opponents are not willing to play football."