The Catalans failed to score at Nou Camp for the first time this season as they now face a tough challenge in the return leg next week.
Barca coach Guardiola was dissatisfied by the performance of German referee Wolfgang Stark amid his opposition's hard-tackling approach.
"It can’t be allowed to happen that the team that tries to play ends up with the same number of cards as the one that just fouls," Guardiola said at the post-match conference.
"The incident with (Michael) Ballack was scandalous. Andres (Iniesta) was heading into the penalty area through on goal. It was a very clear second yellow.
"If the European Champions League is decided by details, as everyone says, then Tuesday’s match is not going to help us."
Iniesta was pulled by Ballack when the Spanish international seemed to be through on Petr Cech.
Philosophy
Guardiola stressed on his team's attack-minded strategy as he admitted that Chelsea's defensive style made it difficult for Barca.
"It's never easy to play well when the opposition is not playing football," said Guardiola.
"The way the team is playing should be taken into account. If one team is attacking then that should count in their favor.
"We are fair. Before the game I said to the players: no hard tackles and no fouls. That was our philosophy."