Chelsea thought they had handed Mourinho a first trophy of his second spell as boss when Eden Hazard netted in extra time after Franck Ribery had cancelled out Fernando Torres' opener.
The dismissal of Ramires for a second bookable offence left the Blues exposed and Javi Martinez tucked in with the final kick of an astonishing game, forcing penalties.
The 2012 European Cup final between the sides had been decided on spot-kicks in Chelsea's favour and on this occasion, shooting towards the boisterous Bayern end, 20-year-old substitute Romelu Lukaku saw his effort saved as the Germans claimed a 5-4 shootout success.
It denied Mourinho a first European Super Cup and a maiden trophy of his second spell at Stamford Bridge.
There had also been personal pride at stake for former Inter Milan and Real Madrid boss Mourinho, who had won three of his previous 15 encounters with Guardiola's Barcelona.
The Spaniard remains his nemesis.
Bayern, treble winners last season and labelled the "perfect" team by Mourinho on the eve of the match, were without influential midfielder Bastian Schweinsteiger due to an ankle injury, but were dominant in an enthralling encounter.
The Blues were on the back foot for most of the evening, but went in front courtesy of a goal on the break.
Restored to start following a striker-less line-up at Manchester United, Torres was at his clinical best in converting Andre Schurrle's cross, showing Mourinho he is prepared to fight new recruit Samuel Eto'o for his place.
Source: PA
Source: PA