A day after Juventus beat Real Madrid 2-1 in the other first leg match, the scale of Barcelona's victory now makes it a runaway favorite to reach the final -- ahead of the return leg against Bayern in Munich on Tuesday.
Guardiola said before the match that there was no way to defend Messi's "magnitude of talent."
And despite keeping him in check for well over an hour, Messi finally proved his former coach right.
After the match, long gone was the smiling Guardiola speaking freely of the good memories that came to him back at Camp Nou on Tuesday.
"It wasn't only Messi. Barca is a very good team," said a dour Guardiola. "The third goal is a shame because with 2-0 we still had options.
"I congratulate Barcelona with all my heart and we will see each other next week in Munich."
Guardiola had also said before the match that he expected no special honors from the fans, who consider him a living club legend for his heaps of trophies as a player and a coach that include three European Cups.
Instead of seeking applause on his return to Camp Nou, the Bayern manager slipped out of the tunnel and turned right -- not left as he had for four seasons from before joining Bayern in 2013 -- to take his place in the opponents' dugout just before kickoff.
But seeing his team in trouble from the start, Guardiola quickly emerged and spent long stretches stalking the sideline, giving orders as he once had to the side in burgundy-and-blue.
Guardiola had already made the risky decision to start Robert Lewandowski, who played with a mask to protect fractures in his upper jaw and Nasal bone, when he also decided to try and stop Messi and his fellow forwards with a three-man defence.
Lewandowski, however, spent long stretches waiting for counterattacks that never happened. And when he had Bayern's first chance in the 18th minute -- and what a chance it was when Barcelona left him unmarked in front of the goal -- he scuffed Thomas Mueller's low ball and sent it trickling well wide.
Guardiola's side might have beaten Barcelona at its own game of ball possession, with 53 per cent to 47 for the hosts, but Barcelona mustered eight shots on goal to none for Bayern.
Led by Messi on the right, Barcelona ran amok at the start.
Not only his usual unstoppable self in attack as he sped through, around and past defenders, Messi was inspired in his pressure and that proved contagious for his entire team as Luis Suarez, Ivan Rakitic and Dani Alves recovered ball after ball inside Bayern's half.
"We created many more chances than our rival, and in a thrilling final 15 minutes we decided the match," said Barcelona coach Luis Enrique, a friend and a former teammate of Guardiola. "Messi is a player of another dimension, but beyond what Leo did in attack, look at how much he ran in defence."
Messi headed on a ball to leave Suarez all alone and with room to move for Barcelona's first opportunity in the 12th, but Neuer made a great save by stretching his right leg to block his low strike.
Neymar was next to rue a miss when, two minutes later, Suarez crossed for the Brazil forward on the edge of the six-yard box, only for Neymar to slip and send the ball off Rafinha and past the wrong side of the post.
Guardiola had seen enough and ordered his team to shift to a four-man back line. The German champions then improved after halftime, and the nerves of both Barcelona's fans and players started to fray.
That was when Messi stepped up.
Messi and Dani Alves combined to put Barcelona in front when the right back recovered the ball from Juan Bernat and laid off for the Argentina international, who put the ball on his left boot and fired a shot between Neuer and the post.
Then, after Rakitic set him up, Messi did it all himself when he used a lightning change of foot to stagger Boateng before lifting a delicate shot over Neuer with his right. That gave him one goal more than Madrid forward Cristiano Ronaldo in Europe's top-tier tournament.
They were also Messi's 52nd and 53rd goals of the season, and they put him one goal ahead of Ronaldo with 10 goals as the top scorer in the Champions League this season.
"Again, Messi leaves us speechless," Barcelona midfielder Andres Iniesta said.
-AP
