Bayern midfielder Bastian Schweinsteiger received a second yellow card late on at Old Trafford, for a lunge at English striker Rooney - with the German collecting the ball, and also his opponent in a rash challenge.
Immediately after the incident, Guardiola intimated Rooney exacerbated the contact as he went down, with Schweinsteiger now suspended for the return leg of the quarter-final at Allianz Arena on April 9.
Guardiola will also be without the services of defender Javi Martinez, who was also cautioned late in Manchester.
But the Spaniard was particularly aggrieved by referee Carlos Velasco Carballo's decision to send off Schweinsteiger.
"Absolutely not," Guardiola responded, when asked if he agreed with the decision.
"I just spoke with the referee and he knows my opinion. He gave me his opinion and I have to respect that.
"To win the Champions League you have to overcome everything, so at times during the competition that happens.
"It's a pity. They are very important players for us. We will try to reach the semi-finals so they can play then."
United boss David Moyes had no concerns with the decision, backing his striker.
"I think Schweinsteiger trips Wayne up. It's a booking - or at least a foul," the former Everton man said.
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