The Spaniard believes that Bayern controlled possession and merited their success thanks to an attacking, positive approach throughout 120 minutes of play.
He told Sky Sports News when presented with Mourinho's claims: "It's his opinion. It's normal, he can say that his team deserved better than what happened.
"I have too my opinion and my opinion after what we have played, we have our behaviour, we have played so, so well; with the ball, without the ball.
"We have played unbelievably good football. The best team won today. We had so many opportunities to score."
Victory in the final earned Guardiola his first piece of silverware since arriving at the Allianz Arena in June, while maintaining his strong record against former La Liga adversary Mourinho.