Bayern and Barca meet at the Nou Camp in Wednesday's Champions League semi-final first leg, with Guardiola back at the Spanish club for the first time since leaving in 2012.
"There is not a system or coach to stop talent of Messi's magnitude," he said.
"The way he has been playing over the past four or five months, you cannot stop him. He is too good."
Messi, 27, scored twice in Barca's 8-0 win over Getafe on Saturday to reach 51 goals for the season, and in November became the Spanish league's all-time top scorer.
Guardiola spent four years as Barca manager from 2008, winning three league titles, two Champions Leagues and two Club World Cups. The 44-year-old also played for the club for 11 years between 1990 and 2001.
"Barca is a very important part of my life," he added. "Until now it was everything but I am here to win. I am not here for a homage but to see Bayern through to the final."
Messi, who will make his 100th European appearance in Wednesday's match, said of Guardiola: "He was with us for a long time and we had the luck to win many titles and experience important moments. He is a coach that studies everything.
"It is the same for both sides. Pep knows us very well and we know what he asks of his players. It is 50-50, we both know each other very well."
Messi also Barca had been "hurt" by their 7-0 aggregate defeat by Bayern in the Champions League semi-finals of 2013.
"That hurt a lot, but a lot of time has passed," said the Argentina forward. "We come into the game differently, as do they, and it will be a different tie to that one."
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