In his former role as Barca boss, Guardiola frequently described Messi as the best player in the world.
He visited Camp Nou as a spectator to watch his former club take apart Manchester City in the last 16 and was pictured in the stands shaking his head in disbelief as Messi wove his magic.
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He now has the opportunity to pitch his Bayern side against the club where he is still idolised for what he achieved as both a player and coach.
If he is to emerge a winner at Camp Nou, he says his side will have to find other ways to beat Barca than trying to cut out the threat of Messi.
"You don't stop Messi, in this form, no," Guardiola told a news conference in Barcelona on Tuesday.
"In the last few months he has been unstoppable. He is too good. Maybe you can try different tactics like getting close to him, making it difficult for him to get the ball, put three players on him but against talent of this size then you cannot defend against it. We will have to look at other ways to win the game."
The Argentine has scored 51 goals in all competitions this season and is part of a formidable attacking trident with Luis Suarez and Neymar. They have notched up 108 goals between them.
Guardiola also feels it would be futile to try and beat Barcelona at their own possession-based game.
"No team has beaten Barcelona for possession. It has always been like that," said the Bayern coach.
"We will do what I think is necessary though and we will see who is in (the final in) Berlin next week.
"It is difficult to find weaknesses in this Barca team which has so much talent but we will try and make the most of our virtues. Barca have talent and they know how to play together."
While Guardiola admits it is likely to be an emotional occasion, he is clear in his mind about what he needs to do.
"It is great to be here and it is impossible not to think of the memories. I knew that if I trained other big teams I would come here with them but I am not here for people to pay homage but to take Bayern to the final," he said.
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