The former Barca boss watched his side beat his old club 3-2 at the Allianz Arena in the semi-final second leg, but they were unable to overturn the 3-0 deficit from the first leg.
And Messi, who scored the first two goals at Camp Nou in the opening clash, was given a sparkling review by his former coach when Guardiola spoke to the media following Bayern’s elimination.
“I am happy that Messi is back here again. He is incredible, he is back to his best as he was when I used to train him,” Guardiola told a press conference.
“We're lucky to live in his age as he is the best player of all time. I can compare him to Pele, and I am very proud of the years I spent with him.”
Guardiola’s side gained a face-saving victory in Munich thanks to an early goal by Medhi Benatia and second-half strikes from Robert Lewandowski and Thomas Muller, but the coach admitted the tie was lost in Catalunya and wished his former charges well in June’s final.
"I am satisfied with the performance of my team. We needed this balance in the Camp Nou but didn’t have it.
"I would like to have played better and have all my best players available to me for my project. I want to congratulate my players. Congrats to Barca also, I hope they win their fifth Champions League final in Berlin."
Bayern were again missing key first-team players Franck Ribery, Arjen Robben and David Alaba at the Allianz Arena. And Guardiola pointed to the absences as one of the reasons for his side’s exit, while also defending his decision to take the game to Barcelona.
"We couldn't hurt Barca at the Camp Nou, because we don't have wingers," he added.
"I’ve always thought, now that I've been knocked out of the Champions League, the only way you can stop players like that is to make them defend. But Barcelona’s third goal last week killed us."