On his 100th appearance in European football, Messi's double moved him back ahead of Cristiano Ronaldo as the all-time leading scorer with 77 in the Champions League and Barca to the brink of their first final in four years.
Manuel Neuer had kept Bayern in the game with a string of fine saves, but was helpless as Messi drilled home the opener from the edge of the area in the 77th minute and then delightfully chipped the German three minutes later.
"The result is a bit harsh. We wanted to control and play our own game," said Bayern boss Guardiola, a former Barca coach.
"Against Barca you can defend deep or play to control. Our control in the first-half worked pretty well, especially in the final 15 minutes.
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Victory takes Barca a step closer to just the second treble of Champions League, La Liga and Copa del Rey in the club's history.
"It brings us closer to a possible final, but we have to confirm it in the second-leg, which will without doubt be a hard game.
"I am very satisfied with how we played and the result against such a strong team. We had a lot of chances and they had very few."
Guardiola is Barca's most successful ever coach having won 14 trophies in four years between 2008 and 2012 and was given a warm reception by the home fans as he took his seat for the first time in the away dugout.