Guardiola said the German was wrong to book Carles Puyol, who is now suspended for next week's second leg, and Yaya Toure and he should have sent off Chelsea's Michael Ballack for a late foul on Andres Iniesta in the dour 0-0 draw at the Nou Camp.
"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 a news conference after the match.
"The incident with Ballack was scandalous," he added. "Andres 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."
Guardiola said the Primera Liga leaders had been the victim of similar refereeing displays all season.
"The way the team is playing should be taken into account," he said. "If one team is attacking then that should count in their favour."
"We are fair. Before the game I said to the players: no hard tackles and no fouls. That was our philosophy."
Guardiola's Chelsea counterpart Guus Hiddink said his side would not necessarily have any advantage from playing at Stamford Bridge in the second leg on May 6.
"Of course we have to improve for the upcoming game," he told a separate news conference.
"These days there is no big advantage playing away or at home so nothing is decided."
The Dutchman paid tribute to his defence, which prevented Barcelona from scoring at home in any competition for the first time since April 23 last year when they were held to a goalless draw by Manchester United at the same stage of the competition.
"Petr (Cech) did a good job defensively and saved the game for us," Hiddink said of his goalkeeper, also praising captain John Terry, Jose Bosingwa, who marked dangerman Lionel Messi, and Florent Malouda.
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