The Catalans reached their first UCL final since 2011, despite Pep Guardiola’s team salvaging their pride in the return leg in Germany.
The German Champions revived their hopes through Medhi Benatia’s early downward header, after losing 3-0 to Barcelona at the Camp Nou last Wednesday.
The Spanish side levelled the score when Luis Suarez squared for a tap-in from Neymar, who drilled a second later in after the pair combined again.
Robert Lewandowski and Thomas Muller both curled in as Bayern won 3-2, but Barca still progressed 5-3 on aggregate after both legs.
However, cross town rivals, Real Madrid, must overturn a 2-1 first-leg deficit against Italian champions-elect, Juventus, at the Santiago Bernabéu Stadium, to defend the European championship title against Barca.