Barcelona, who are in the last four for the seventh time in eight seasons, will be at home to the Bundesliga side in the first leg on May 6 with the return at the Allianz Arena on May 12.
Guardiola won the European Cup as a player with Barcelona in 1992 and then won 14 trophies in four seasons as coach, including the Champions League in 2009 and 2011.
"When you play in the semi-finals, you always get a big team. I have great respect for them and I am very, very happy to have had this experience in my life, but at the end of the day it's a football match," said Guardiola.
"Of course it is special for me and very, very emotional, whether it is one game or two."
"Of course, only football can write stories like this," remarked Bayern's sporting director Matthias Sammer.
After leaving in 2012, Guardiola did not go back to the Camp Nou until he attended Barcelona's victory over Manchester City in the last 16 last month.
His old side are now coached by Luis Enrique, alongside whom he played at Barcelona in the 1990s.
"It is a special game because Pep is on the other side. It will be the first time that he has faced his Barca, it will be the first time that I have faced him as a coach which will be special for me, and I am sure it will be for my players," said Luis Enrique, who did not seem too concerned about having to play the first leg at home.
