The Primera Liga leaders will face Guus Hiddink's side next after they brushed aside Bayern Munich and the Blues got the better of Liverpool.
The pair will now meet in the semi-finals of the competition just two games away from an appearance at this year's final in Rome on May 27.
Guardiola knew he would face either Chelsea or Liverpool in the semis, but now concedes he did not have a preference on who he would rather face.
"I don't think we had any preference between Liverpool or Chelsea," he said. "Maybe Chelsea are more attacking, but Liverpool are very disciplined in defence.
"Either way, we have a tough opponent and we have got to accept that it is Chelsea and not Liverpool. Liverpool would not have been any easier, but Chelsea is hard enough."
Bayern boss Jurgen Klinsmann has admitted his troops harboured faint hopes of overturning their daunting 4-0 first leg deficit to Barcelona.
Frank Ribery pulled a goal back for Bayern shortly after half-time, although their hopes were extinguished when Seydou Keita levelled.
Klinsmann had no complaints over the two legs stating that the better team had clearly progressed.
"Yes, we had a small hope, even if we did not say so," he said.
"We had a meeting three hours before kick-off and we said that we can dream if we approach the game well and give it everything.
"There have been crazy stories in football and when we went 1-0 up there was a bit of hope. But after they made it 1-1, it was over.
"We had set our sights as high as possible and we did a lot, but we have been knocked out by a team who are clearly better.
"They are the best club in world football at the moment and we have seen that we have a lot of work to do if we are to go further next year."