Messi inspired Barca to a 3-0 first-leg victory that Bayern could not overturn, despite a 3-2 win in the return game.
“He is the best player of all time, I compare him with Pele,” said Guardiola, 44. “I hope Barca win their fifth Champions League final.”
Barca will play Real Madrid or Juventus in the final in Berlin on 6 June.
Brazil forward Neymar scored twice in the Allianz Arena to give the Spanish league leaders a 5-1 aggregate lead before Bayern fought back to win on the night.
But Guardiola reserved his praise for Argentina skipper Messi, who turned the semi-final in Barca’s favour with a late brace at the Nou Camp last week.
Messi has scored 53 goals so far this season after admitting his previous campaign, where he netted 44 times despite injuries and allegations of tax fraud, was “difficult”.
“He is back, he is there where I had the privilege to train him,” said Guardiola, who – along with Messi – won 14 trophies in his four seasons in charge at Barcelona between 2008 and 2012. “He is definitely back at his best.”